Starting phenix.real_space_refine
on Tue Jun 10 19:28:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ze3_60022/06_2025/8ze3_60022_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ze3_60022/06_2025/8ze3_60022.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ze3_60022/06_2025/8ze3_60022.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ze3_60022/06_2025/8ze3_60022.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ze3_60022/06_2025/8ze3_60022_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ze3_60022/06_2025/8ze3_60022_trim.cif"
  }
  resolution = 3.17
  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=   0.017 sd=   0.119
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      80      5.16       5
     C    7868      2.51       5
     N    2012      2.21       5
     O    2112      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12072
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 3006
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 6, 'TRANS': 367}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 3006
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 6, 'TRANS': 367}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 3006
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 6, 'TRANS': 367}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 3006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 3006
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 6, 'TRANS': 367}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'FRU': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'FRU': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'FRU': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'FRU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.46, per 1000 atoms: 0.62
  Number of scatterers: 12072
  At special positions: 0
  Unit cell: (97.86, 97.86, 98.792, 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      80     16.00
     O    2112      8.00
     N    2012      7.00
     C    7868      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.95
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2864

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      83.7% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
    Processing helix  chain 'A' and resid 37 through 64
      removed outlier: 3.505A  pdb=" N   ILE A  42 " --> pdb=" O   TRP A  38 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR A  43 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 100
      removed outlier: 4.009A  pdb=" N   VAL A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 118
      removed outlier: 3.576A  pdb=" N   THR A 118 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 161
      removed outlier: 3.792A  pdb=" N   ASP A 128 " --> pdb=" O   ASN A 124 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET A 161 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 174
    Processing helix  chain 'A' and resid 175 through 214
      removed outlier: 3.553A  pdb=" N   LEU A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   TYR A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 292
      removed outlier: 4.168A  pdb=" N   SER A 268 " --> pdb=" O   THR A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 321
      removed outlier: 3.729A  pdb=" N   ALA A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 342
      removed outlier: 3.936A  pdb=" N   VAL A 327 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 357
    Processing helix  chain 'A' and resid 358 through 368
      removed outlier: 4.929A  pdb=" N   GLU A 364 " --> pdb=" O   GLN A 360 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE A 365 " --> pdb=" O   ILE A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 388
      removed outlier: 3.711A  pdb=" N   GLU A 376 " --> pdb=" O   PRO A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 424
      removed outlier: 3.690A  pdb=" N   THR A 406 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR A 414 " --> pdb=" O   SER A 410 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE A 420 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 17
    Processing helix  chain 'B' and resid 37 through 64
      removed outlier: 3.505A  pdb=" N   ILE B  42 " --> pdb=" O   TRP B  38 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   TYR B  43 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 100
      removed outlier: 4.009A  pdb=" N   VAL B  78 " --> pdb=" O   ALA B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 118
      removed outlier: 3.576A  pdb=" N   THR B 118 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 161
      removed outlier: 3.793A  pdb=" N   ASP B 128 " --> pdb=" O   ASN B 124 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET B 161 " --> pdb=" O   MET B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 174
    Processing helix  chain 'B' and resid 175 through 214
      removed outlier: 3.553A  pdb=" N   LEU B 210 " --> pdb=" O   LEU B 206 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR B 214 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 292
      removed outlier: 4.168A  pdb=" N   SER B 268 " --> pdb=" O   THR B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 321
      removed outlier: 3.729A  pdb=" N   ALA B 311 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 342
      removed outlier: 3.936A  pdb=" N   VAL B 327 " --> pdb=" O   ASP B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 357
    Processing helix  chain 'B' and resid 358 through 368
      removed outlier: 4.929A  pdb=" N   GLU B 364 " --> pdb=" O   GLN B 360 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE B 365 " --> pdb=" O   ILE B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 388
      removed outlier: 3.709A  pdb=" N   GLU B 376 " --> pdb=" O   PRO B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 424
      removed outlier: 3.690A  pdb=" N   THR B 406 " --> pdb=" O   ARG B 402 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR B 414 " --> pdb=" O   SER B 410 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE B 420 " --> pdb=" O   LEU B 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 17
    Processing helix  chain 'C' and resid 37 through 64
      removed outlier: 3.505A  pdb=" N   ILE C  42 " --> pdb=" O   TRP C  38 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR C  43 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 100
      removed outlier: 4.010A  pdb=" N   VAL C  78 " --> pdb=" O   ALA C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 118
      removed outlier: 3.576A  pdb=" N   THR C 118 " --> pdb=" O   LYS C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 161
      removed outlier: 3.792A  pdb=" N   ASP C 128 " --> pdb=" O   ASN C 124 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET C 161 " --> pdb=" O   MET C 157 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 174
    Processing helix  chain 'C' and resid 175 through 214
      removed outlier: 3.553A  pdb=" N   LEU C 210 " --> pdb=" O   LEU C 206 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   TYR C 214 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 292
      removed outlier: 4.168A  pdb=" N   SER C 268 " --> pdb=" O   THR C 264 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 321
      removed outlier: 3.730A  pdb=" N   ALA C 311 " --> pdb=" O   LEU C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 342
      removed outlier: 3.937A  pdb=" N   VAL C 327 " --> pdb=" O   ASP C 323 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 357
    Processing helix  chain 'C' and resid 358 through 368
      removed outlier: 4.929A  pdb=" N   GLU C 364 " --> pdb=" O   GLN C 360 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE C 365 " --> pdb=" O   ILE C 361 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 388
      removed outlier: 3.710A  pdb=" N   GLU C 376 " --> pdb=" O   PRO C 372 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 424
      removed outlier: 3.690A  pdb=" N   THR C 406 " --> pdb=" O   ARG C 402 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR C 414 " --> pdb=" O   SER C 410 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ILE C 420 " --> pdb=" O   LEU C 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 17
    Processing helix  chain 'D' and resid 37 through 64
      removed outlier: 3.505A  pdb=" N   ILE D  42 " --> pdb=" O   TRP D  38 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR D  43 " --> pdb=" O   LEU D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 100
      removed outlier: 4.009A  pdb=" N   VAL D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 118
      removed outlier: 3.577A  pdb=" N   THR D 118 " --> pdb=" O   LYS D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 124 through 161
      removed outlier: 3.792A  pdb=" N   ASP D 128 " --> pdb=" O   ASN D 124 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET D 161 " --> pdb=" O   MET D 157 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 174
    Processing helix  chain 'D' and resid 175 through 214
      removed outlier: 3.552A  pdb=" N   LEU D 210 " --> pdb=" O   LEU D 206 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR D 214 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 292
      removed outlier: 4.168A  pdb=" N   SER D 268 " --> pdb=" O   THR D 264 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 321
      removed outlier: 3.730A  pdb=" N   ALA D 311 " --> pdb=" O   LEU D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 342
      removed outlier: 3.937A  pdb=" N   VAL D 327 " --> pdb=" O   ASP D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 344 through 357
    Processing helix  chain 'D' and resid 358 through 368
      removed outlier: 4.930A  pdb=" N   GLU D 364 " --> pdb=" O   GLN D 360 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE D 365 " --> pdb=" O   ILE D 361 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 388
      removed outlier: 3.710A  pdb=" N   GLU D 376 " --> pdb=" O   PRO D 372 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 402 through 424
      removed outlier: 3.690A  pdb=" N   THR D 406 " --> pdb=" O   ARG D 402 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR D 414 " --> pdb=" O   SER D 410 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE D 420 " --> pdb=" O   LEU D 416 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 27
      removed outlier: 4.255A  pdb=" N   ASN A  27 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 5.175A  pdb=" N   GLN A  31 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 27
      removed outlier: 4.254A  pdb=" N   ASN B  27 " --> pdb=" O   GLN B  31 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   GLN B  31 " --> pdb=" O   ASN B  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 27
      removed outlier: 4.254A  pdb=" N   ASN C  27 " --> pdb=" O   GLN C  31 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   GLN C  31 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 27
      removed outlier: 4.255A  pdb=" N   ASN D  27 " --> pdb=" O   GLN D  31 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   GLN D  31 " --> pdb=" O   ASN D  27 " (cutoff:3.500A)

    976 hydrogen bonds defined for protein.
    2928 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: 3.36

  Time building geometry restraints manager: 3.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3724
        1.35 -     1.47: 3043
        1.47 -     1.58: 5409
        1.58 -     1.70: 0
        1.70 -     1.82: 128
  Bond restraints: 12304
  Sorted by residual:
  bond pdb=" C2  FRU B 501 "
       pdb=" C3  FRU B 501 "
    ideal  model  delta    sigma   weight residual
    1.541  1.463  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C2  FRU C 501 "
       pdb=" C3  FRU C 501 "
    ideal  model  delta    sigma   weight residual
    1.541  1.463  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C2  FRU A 501 "
       pdb=" C3  FRU A 501 "
    ideal  model  delta    sigma   weight residual
    1.541  1.463  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C2  FRU D 501 "
       pdb=" C3  FRU D 501 "
    ideal  model  delta    sigma   weight residual
    1.541  1.463  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C3  FRU C 501 "
       pdb=" C4  FRU C 501 "
    ideal  model  delta    sigma   weight residual
    1.519  1.458  0.061 2.00e-02 2.50e+03 9.36e+00
  ... (remaining 12299 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 16312
        1.83 -     3.66: 241
        3.66 -     5.49: 67
        5.49 -     7.32: 28
        7.32 -     9.15: 12
  Bond angle restraints: 16660
  Sorted by residual:
  angle pdb=" CA  GLU C 376 "
        pdb=" CB  GLU C 376 "
        pdb=" CG  GLU C 376 "
      ideal   model   delta    sigma   weight residual
     114.10  120.37   -6.27 2.00e+00 2.50e-01 9.81e+00
  angle pdb=" CA  GLU D 376 "
        pdb=" CB  GLU D 376 "
        pdb=" CG  GLU D 376 "
      ideal   model   delta    sigma   weight residual
     114.10  120.36   -6.26 2.00e+00 2.50e-01 9.81e+00
  angle pdb=" CA  GLU A 376 "
        pdb=" CB  GLU A 376 "
        pdb=" CG  GLU A 376 "
      ideal   model   delta    sigma   weight residual
     114.10  120.35   -6.25 2.00e+00 2.50e-01 9.76e+00
  angle pdb=" CA  GLU B 376 "
        pdb=" CB  GLU B 376 "
        pdb=" CG  GLU B 376 "
      ideal   model   delta    sigma   weight residual
     114.10  120.32   -6.22 2.00e+00 2.50e-01 9.67e+00
  angle pdb=" C2  FRU D 501 "
        pdb=" O5  FRU D 501 "
        pdb=" C5  FRU D 501 "
      ideal   model   delta    sigma   weight residual
     112.00  102.85    9.15 3.00e+00 1.11e-01 9.31e+00
  ... (remaining 16655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 6136
       17.84 -    35.68: 896
       35.68 -    53.52: 292
       53.52 -    71.36: 56
       71.36 -    89.20: 20
  Dihedral angle restraints: 7400
    sinusoidal: 2984
      harmonic: 4416
  Sorted by residual:
  dihedral pdb=" CA  LYS A  26 "
           pdb=" C   LYS A  26 "
           pdb=" N   ASN A  27 "
           pdb=" CA  ASN A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.84   17.16     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  LYS B  26 "
           pdb=" C   LYS B  26 "
           pdb=" N   ASN B  27 "
           pdb=" CA  ASN B  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.86   17.14     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CA  LYS C  26 "
           pdb=" C   LYS C  26 "
           pdb=" N   ASN C  27 "
           pdb=" CA  ASN C  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.86   17.14     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 7397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1370
       0.032 -    0.065: 404
       0.065 -    0.097: 182
       0.097 -    0.129: 20
       0.129 -    0.162: 8
  Chirality restraints: 1984
  Sorted by residual:
  chirality pdb=" CG  LEU D  60 "
            pdb=" CB  LEU D  60 "
            pdb=" CD1 LEU D  60 "
            pdb=" CD2 LEU D  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.53e-01
  chirality pdb=" CG  LEU C  60 "
            pdb=" CB  LEU C  60 "
            pdb=" CD1 LEU C  60 "
            pdb=" CD2 LEU C  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CG  LEU A  60 "
            pdb=" CB  LEU A  60 "
            pdb=" CD1 LEU A  60 "
            pdb=" CD2 LEU A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.38e-01
  ... (remaining 1981 not shown)

  Planarity restraints: 2008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 376 "    0.006 2.00e-02 2.50e+03   1.31e-02 1.71e+00
        pdb=" CD  GLU B 376 "   -0.023 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 376 "    0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 376 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 376 "    0.006 2.00e-02 2.50e+03   1.28e-02 1.65e+00
        pdb=" CD  GLU C 376 "   -0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 376 "    0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 376 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D 376 "   -0.006 2.00e-02 2.50e+03   1.27e-02 1.63e+00
        pdb=" CD  GLU D 376 "    0.022 2.00e-02 2.50e+03
        pdb=" OE1 GLU D 376 "   -0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU D 376 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 2005 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 138
        2.63 -     3.20: 10906
        3.20 -     3.77: 20108
        3.77 -     4.33: 25412
        4.33 -     4.90: 43261
  Nonbonded interactions: 99825
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 279 "
            pdb=" NH2 ARG B 367 "
     model   vdw
     2.064 3.120
  nonbonded pdb=" NH2 ARG A 367 "
            pdb=" OE1 GLU D 279 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" O   THR B 212 "
            pdb=" OG  SER B 216 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   THR D 212 "
            pdb=" OG  SER D 216 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" O   THR C 212 "
            pdb=" OG  SER C 216 "
     model   vdw
     2.179 3.040
  ... (remaining 99820 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  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:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     28.040
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
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      :  0.004   0.078  12304  Z= 0.193
  Angle     :  0.683   9.152  16660  Z= 0.348
  Chirality :  0.038   0.162   1984
  Planarity :  0.004   0.046   2008
  Dihedral  : 19.034  89.200   4536
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 34.70 %
    Favored  : 62.42 %
  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:  1.13 (0.22), residues: 1472
  helix:  1.45 (0.14), residues: 1224
  sheet: -1.39 (0.74), residues: 40
  loop : -2.98 (0.37), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 328 
 HIS   0.003   0.001   HIS A 278 
 PHE   0.008   0.001   PHE A 192 
 TYR   0.013   0.001   TYR D 326 
 ARG   0.008   0.000   ARG D 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10926 (  976)
  hydrogen bonds       : angle       5.29952 ( 2928)
  covalent geometry    : bond        0.00388 (12304)
  covalent geometry    : angle       0.68328 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 252
  time to evaluate  : 1.351 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6854 (p0) cc_final: 0.6505 (m-40)
REVERT: B  209 MET cc_start: 0.7656 (tpp) cc_final: 0.7357 (tpt)
REVERT: C   22 TYR cc_start: 0.7935 (m-80) cc_final: 0.7570 (m-10)
REVERT: C  116 ASP cc_start: 0.7833 (m-30) cc_final: 0.7582 (m-30)
REVERT: D  103 ARG cc_start: 0.7194 (tpp-160) cc_final: 0.6774 (mmm-85)
REVERT: D  129 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7422 (ttm170)
REVERT: D  208 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7103 (tp-100)
REVERT: D  324 ASN cc_start: 0.6881 (p0) cc_final: 0.6576 (m-40)
  outliers start: 38
  outliers final: 32
  residues processed: 290
  average time/residue: 0.2486
  time to fit residues: 101.3444
Evaluate side-chains
  253 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 221
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  383 GLN
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  280 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  383 GLN
Chi-restraints excluded: chain B residue  417 VAL
Chi-restraints excluded: chain C residue    7 ASN
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue  155 VAL
Chi-restraints excluded: chain C residue  280 SER
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  383 GLN
Chi-restraints excluded: chain C residue  417 VAL
Chi-restraints excluded: chain D residue    7 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   37 SER
Chi-restraints excluded: chain D residue  155 VAL
Chi-restraints excluded: chain D residue  182 TYR
Chi-restraints excluded: chain D residue  280 SER
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  383 GLN
Chi-restraints excluded: chain D residue  417 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 116 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A 278 HIS
A 330 GLN
A 384 GLN
B   7 ASN
B 278 HIS
B 330 GLN
C 278 HIS
C 330 GLN
D 278 HIS
D 330 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.167919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.129484 restraints weight = 14278.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.17
r_work: 0.3268 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12304  Z= 0.131
  Angle     :  0.512   7.847  16660  Z= 0.262
  Chirality :  0.037   0.224   1984
  Planarity :  0.003   0.026   2008
  Dihedral  :  7.245  58.035   1784
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 26.89 %
    Favored  : 68.48 %
  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:  1.96 (0.22), residues: 1472
  helix:  2.06 (0.14), residues: 1228
  sheet: -1.72 (0.72), residues: 40
  loop : -3.00 (0.37), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 328 
 HIS   0.003   0.001   HIS A 189 
 PHE   0.015   0.001   PHE C 192 
 TYR   0.007   0.001   TYR C 182 
 ARG   0.004   0.000   ARG A 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03925 (  976)
  hydrogen bonds       : angle       3.73006 ( 2928)
  covalent geometry    : bond        0.00295 (12304)
  covalent geometry    : angle       0.51165 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 238
  time to evaluate  : 1.448 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.7097 (p0) cc_final: 0.6776 (m-40)
REVERT: A  330 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.6835 (mp-120)
REVERT: B   93 THR cc_start: 0.8998 (m) cc_final: 0.8751 (m)
REVERT: B  145 ILE cc_start: 0.8391 (mp) cc_final: 0.8045 (mp)
REVERT: B  324 ASN cc_start: 0.7299 (p0) cc_final: 0.6825 (m-40)
REVERT: B  330 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7003 (mp-120)
REVERT: B  346 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8215 (tp30)
REVERT: C  324 ASN cc_start: 0.7061 (p0) cc_final: 0.6657 (m-40)
REVERT: C  330 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7138 (mp-120)
REVERT: D  116 ASP cc_start: 0.8320 (m-30) cc_final: 0.8072 (m-30)
REVERT: D  129 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7890 (ttm170)
REVERT: D  145 ILE cc_start: 0.8266 (mp) cc_final: 0.7912 (mp)
REVERT: D  324 ASN cc_start: 0.7082 (p0) cc_final: 0.6785 (m-40)
REVERT: D  330 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.6831 (mp-120)
  outliers start: 61
  outliers final: 34
  residues processed: 281
  average time/residue: 0.2460
  time to fit residues: 100.9652
Evaluate side-chains
  254 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 216
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  330 GLN
Chi-restraints excluded: chain A residue  343 MET
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain B residue    7 ASN
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  330 GLN
Chi-restraints excluded: chain B residue  343 MET
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  330 GLN
Chi-restraints excluded: chain C residue  343 MET
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  283 LYS
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  330 GLN
Chi-restraints excluded: chain D residue  343 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:    0.0470
   chunk 42 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 126 optimal weight:    6.9990
   chunk 140 optimal weight:    0.7980
   chunk 110 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.1080

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A 330 GLN
A 383 GLN
B 330 GLN
C 330 GLN
C 383 GLN
C 384 GLN
D 330 GLN
D 384 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.166269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.127512 restraints weight = 14330.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.18
r_work: 0.3255 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12304  Z= 0.132
  Angle     :  0.496   7.510  16660  Z= 0.256
  Chirality :  0.036   0.137   1984
  Planarity :  0.003   0.025   2008
  Dihedral  :  4.984  40.930   1744
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 25.61 %
    Favored  : 69.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.14 (0.22), residues: 1472
  helix:  2.21 (0.14), residues: 1228
  sheet: -2.03 (0.64), residues: 40
  loop : -3.00 (0.37), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 328 
 HIS   0.004   0.001   HIS D 189 
 PHE   0.012   0.001   PHE B 192 
 TYR   0.013   0.001   TYR B 326 
 ARG   0.005   0.000   ARG D 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03819 (  976)
  hydrogen bonds       : angle       3.58668 ( 2928)
  covalent geometry    : bond        0.00300 (12304)
  covalent geometry    : angle       0.49601 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 230
  time to evaluate  : 1.362 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.7123 (p0) cc_final: 0.6768 (m-40)
REVERT: A  330 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.6791 (mp-120)
REVERT: B   93 THR cc_start: 0.9022 (m) cc_final: 0.8812 (m)
REVERT: B  145 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8085 (mp)
REVERT: B  209 MET cc_start: 0.8290 (tpp) cc_final: 0.8049 (tpt)
REVERT: B  324 ASN cc_start: 0.7283 (p0) cc_final: 0.6859 (m-40)
REVERT: B  330 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.6913 (mp-120)
REVERT: C   33 GLU cc_start: 0.7788 (tt0) cc_final: 0.7408 (pt0)
REVERT: C  324 ASN cc_start: 0.7057 (p0) cc_final: 0.6640 (m-40)
REVERT: C  330 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7115 (mp-120)
REVERT: C  376 GLU cc_start: 0.7994 (tp30) cc_final: 0.7787 (tp30)
REVERT: D  116 ASP cc_start: 0.8372 (m-30) cc_final: 0.8061 (m-30)
REVERT: D  129 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7838 (ttm170)
REVERT: D  145 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: D  324 ASN cc_start: 0.6939 (p0) cc_final: 0.6618 (m-40)
  outliers start: 65
  outliers final: 35
  residues processed: 273
  average time/residue: 0.2163
  time to fit residues: 87.5537
Evaluate side-chains
  243 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 203
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  330 GLN
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  330 GLN
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  330 GLN
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  361 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 143 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 145 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
A 330 GLN
B 173 GLN
B 330 GLN
C   7 ASN
C 330 GLN
D   7 ASN
D 330 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.114730 restraints weight = 14108.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.30
r_work: 0.3130 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12304  Z= 0.226
  Angle     :  0.557   8.194  16660  Z= 0.292
  Chirality :  0.040   0.289   1984
  Planarity :  0.003   0.023   2008
  Dihedral  :  4.858  47.349   1744
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 25.15 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.21), residues: 1472
  helix:  2.12 (0.14), residues: 1228
  sheet: -1.89 (0.66), residues: 40
  loop : -3.08 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 328 
 HIS   0.004   0.001   HIS D 189 
 PHE   0.016   0.001   PHE C 192 
 TYR   0.012   0.002   TYR D 214 
 ARG   0.005   0.000   ARG C 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  976)
  hydrogen bonds       : angle       3.72183 ( 2928)
  covalent geometry    : bond        0.00541 (12304)
  covalent geometry    : angle       0.55726 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 209
  time to evaluate  : 1.298 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.8286 (m-30) cc_final: 0.7980 (m-30)
REVERT: A  209 MET cc_start: 0.8218 (tpp) cc_final: 0.7952 (tpt)
REVERT: A  324 ASN cc_start: 0.7072 (p0) cc_final: 0.6639 (m-40)
REVERT: B  145 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8256 (mt)
REVERT: B  182 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8343 (m-80)
REVERT: B  209 MET cc_start: 0.8417 (tpp) cc_final: 0.8208 (tpt)
REVERT: B  324 ASN cc_start: 0.7119 (p0) cc_final: 0.6654 (m-40)
REVERT: C  182 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8358 (m-80)
REVERT: C  209 MET cc_start: 0.8496 (tpp) cc_final: 0.8278 (tpt)
REVERT: C  324 ASN cc_start: 0.6946 (p0) cc_final: 0.6467 (m-40)
REVERT: C  376 GLU cc_start: 0.7997 (tp30) cc_final: 0.7710 (tp30)
REVERT: D  129 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7761 (ttm170)
REVERT: D  145 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8280 (mt)
REVERT: D  209 MET cc_start: 0.8465 (tpp) cc_final: 0.8265 (tpt)
REVERT: D  324 ASN cc_start: 0.6911 (p0) cc_final: 0.6522 (m-40)
REVERT: D  376 GLU cc_start: 0.8008 (tp30) cc_final: 0.7727 (tp30)
  outliers start: 67
  outliers final: 40
  residues processed: 259
  average time/residue: 0.2216
  time to fit residues: 84.2905
Evaluate side-chains
  237 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 193
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  369 VAL
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  283 LYS
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  283 LYS
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  361 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 58 optimal weight:    0.1980
   chunk 146 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 125 optimal weight:    0.9990
   chunk 142 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 127 optimal weight:    6.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
B 173 GLN
C   7 ASN
C 173 GLN
D   7 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.161832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.119984 restraints weight = 14163.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.33
r_work: 0.3201 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12304  Z= 0.113
  Angle     :  0.475   8.365  16660  Z= 0.244
  Chirality :  0.036   0.252   1984
  Planarity :  0.003   0.026   2008
  Dihedral  :  4.335  37.426   1744
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 26.67 %
    Favored  : 68.94 %
  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:  2.38 (0.22), residues: 1472
  helix:  2.38 (0.14), residues: 1228
  sheet: -1.87 (0.67), residues: 40
  loop : -3.04 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.009   0.001   PHE C 192 
 TYR   0.012   0.001   TYR D 214 
 ARG   0.003   0.000   ARG C 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03651 (  976)
  hydrogen bonds       : angle       3.43527 ( 2928)
  covalent geometry    : bond        0.00251 (12304)
  covalent geometry    : angle       0.47532 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 224
  time to evaluate  : 1.411 
Fit side-chains
REVERT: A  116 ASP cc_start: 0.8258 (m-30) cc_final: 0.8002 (m-30)
REVERT: A  324 ASN cc_start: 0.7022 (p0) cc_final: 0.6544 (m-40)
REVERT: A  376 GLU cc_start: 0.7927 (tp30) cc_final: 0.7551 (tp30)
REVERT: A  397 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8482 (mt)
REVERT: B  145 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8195 (mt)
REVERT: B  182 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.8152 (m-80)
REVERT: B  209 MET cc_start: 0.8389 (tpp) cc_final: 0.8185 (tpt)
REVERT: B  324 ASN cc_start: 0.6968 (p0) cc_final: 0.6559 (m110)
REVERT: B  397 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8459 (mt)
REVERT: C  364 GLU cc_start: 0.7068 (mp0) cc_final: 0.6730 (mp0)
REVERT: C  376 GLU cc_start: 0.7957 (tp30) cc_final: 0.7604 (tp30)
REVERT: C  397 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8452 (mt)
REVERT: D  129 ARG cc_start: 0.8047 (ttm170) cc_final: 0.7717 (ttm170)
REVERT: D  145 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: D  376 GLU cc_start: 0.7980 (tp30) cc_final: 0.7630 (tp30)
REVERT: D  397 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8503 (mt)
  outliers start: 58
  outliers final: 32
  residues processed: 264
  average time/residue: 0.2238
  time to fit residues: 86.1349
Evaluate side-chains
  239 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 200
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ASN
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   72 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain C residue    7 ASN
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   72 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  361 ILE
Chi-restraints excluded: chain D residue  397 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 121 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   chunk 130 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 142 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A   7 ASN
B 173 GLN
C   7 ASN
C 173 GLN
D   7 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.115297 restraints weight = 14332.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.30
r_work: 0.3137 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12304  Z= 0.197
  Angle     :  0.543   8.623  16660  Z= 0.281
  Chirality :  0.039   0.247   1984
  Planarity :  0.003   0.023   2008
  Dihedral  :  4.165  36.452   1740
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 27.65 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.21), residues: 1472
  helix:  2.28 (0.14), residues: 1228
  sheet: -1.65 (0.68), residues: 40
  loop : -3.08 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.014   0.001   PHE C 192 
 TYR   0.011   0.001   TYR B  22 
 ARG   0.004   0.000   ARG C 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04317 (  976)
  hydrogen bonds       : angle       3.59309 ( 2928)
  covalent geometry    : bond        0.00471 (12304)
  covalent geometry    : angle       0.54294 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 209
  time to evaluate  : 1.470 
Fit side-chains
REVERT: A  209 MET cc_start: 0.8380 (tpp) cc_final: 0.8176 (tpt)
REVERT: A  324 ASN cc_start: 0.6959 (p0) cc_final: 0.6469 (m-40)
REVERT: A  376 GLU cc_start: 0.7983 (tp30) cc_final: 0.7591 (tp30)
REVERT: B  145 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8221 (mt)
REVERT: B  182 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8412 (m-80)
REVERT: B  209 MET cc_start: 0.8427 (tpp) cc_final: 0.8194 (tpt)
REVERT: B  324 ASN cc_start: 0.7039 (p0) cc_final: 0.6607 (m-40)
REVERT: B  397 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8508 (mp)
REVERT: C  157 MET cc_start: 0.8343 (mtp) cc_final: 0.7616 (mtp)
REVERT: C  161 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5762 (pmt)
REVERT: C  376 GLU cc_start: 0.7941 (tp30) cc_final: 0.7565 (tp30)
REVERT: C  397 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (mp)
REVERT: D   33 GLU cc_start: 0.7862 (tt0) cc_final: 0.7407 (pt0)
REVERT: D  129 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7791 (ttm170)
REVERT: D  145 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8267 (mt)
REVERT: D  182 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8401 (m-80)
REVERT: D  324 ASN cc_start: 0.6989 (p0) cc_final: 0.6543 (m-40)
REVERT: D  376 GLU cc_start: 0.7952 (tp30) cc_final: 0.7591 (tp30)
  outliers start: 58
  outliers final: 37
  residues processed: 252
  average time/residue: 0.2375
  time to fit residues: 86.5130
Evaluate side-chains
  246 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 202
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  283 LYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   72 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  182 TYR
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  361 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 143 optimal weight:    4.9990
   chunk 141 optimal weight:    1.9990
   chunk 37 optimal weight:   10.0000
   chunk 136 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 113 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 278 HIS
B 173 GLN
C 173 GLN
D   7 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.162434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.124270 restraints weight = 14343.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 2.18
r_work: 0.3010 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12304  Z= 0.152
  Angle     :  0.520   9.644  16660  Z= 0.265
  Chirality :  0.038   0.303   1984
  Planarity :  0.003   0.026   2008
  Dihedral  :  3.933  36.985   1738
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 27.80 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.22), residues: 1472
  helix:  2.36 (0.14), residues: 1228
  sheet: -1.59 (0.68), residues: 40
  loop : -3.07 (0.37), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.011   0.001   PHE C 192 
 TYR   0.010   0.001   TYR D 214 
 ARG   0.003   0.000   ARG C 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  976)
  hydrogen bonds       : angle       3.51788 ( 2928)
  covalent geometry    : bond        0.00357 (12304)
  covalent geometry    : angle       0.51974 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 205
  time to evaluate  : 1.423 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6768 (p0) cc_final: 0.6310 (m-40)
REVERT: A  376 GLU cc_start: 0.8080 (tp30) cc_final: 0.7672 (tp30)
REVERT: A  397 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8554 (mp)
REVERT: B  145 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8259 (mt)
REVERT: B  182 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8377 (m-80)
REVERT: B  324 ASN cc_start: 0.6915 (p0) cc_final: 0.6447 (m110)
REVERT: B  397 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8564 (mp)
REVERT: C  157 MET cc_start: 0.8147 (mtp) cc_final: 0.7457 (mtp)
REVERT: C  161 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5830 (pmt)
REVERT: C  182 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8356 (m-80)
REVERT: C  364 GLU cc_start: 0.7266 (mp0) cc_final: 0.7055 (mp0)
REVERT: C  376 GLU cc_start: 0.7943 (tp30) cc_final: 0.7546 (tp30)
REVERT: C  397 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8599 (mt)
REVERT: D  145 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8272 (mt)
REVERT: D  157 MET cc_start: 0.8288 (mtp) cc_final: 0.7464 (mtp)
REVERT: D  376 GLU cc_start: 0.7983 (tp30) cc_final: 0.7607 (tp30)
REVERT: D  397 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8583 (mp)
  outliers start: 61
  outliers final: 37
  residues processed: 252
  average time/residue: 0.2258
  time to fit residues: 83.1683
Evaluate side-chains
  244 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 198
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   72 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   72 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain D residue    7 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  361 ILE
Chi-restraints excluded: chain D residue  397 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 123 optimal weight:    6.9990
   chunk 117 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 121 optimal weight:    4.9990
   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 423 GLN
B 173 GLN
C 173 GLN
D   7 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.161436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.123201 restraints weight = 14396.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.18
r_work: 0.2995 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2846 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12304  Z= 0.174
  Angle     :  0.552   9.991  16660  Z= 0.277
  Chirality :  0.039   0.346   1984
  Planarity :  0.003   0.027   2008
  Dihedral  :  3.938  36.926   1738
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 28.56 %
    Favored  : 67.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.30 (0.22), residues: 1472
  helix:  2.33 (0.14), residues: 1228
  sheet: -1.46 (0.69), residues: 40
  loop : -3.13 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.012   0.001   PHE C 192 
 TYR   0.010   0.001   TYR B 214 
 ARG   0.003   0.000   ARG C 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04130 (  976)
  hydrogen bonds       : angle       3.56867 ( 2928)
  covalent geometry    : bond        0.00412 (12304)
  covalent geometry    : angle       0.55172 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 196
  time to evaluate  : 1.436 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6754 (p0) cc_final: 0.6291 (m-40)
REVERT: A  376 GLU cc_start: 0.8076 (tp30) cc_final: 0.7653 (tp30)
REVERT: B  145 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8216 (mt)
REVERT: B  157 MET cc_start: 0.8182 (mtp) cc_final: 0.7464 (mtp)
REVERT: B  161 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5842 (pmt)
REVERT: B  182 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8426 (m-80)
REVERT: B  324 ASN cc_start: 0.6905 (p0) cc_final: 0.6432 (m110)
REVERT: B  397 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8591 (mp)
REVERT: C  157 MET cc_start: 0.8172 (mtp) cc_final: 0.7483 (mtp)
REVERT: C  161 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5847 (pmt)
REVERT: C  182 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8373 (m-80)
REVERT: C  364 GLU cc_start: 0.7350 (mp0) cc_final: 0.7122 (mp0)
REVERT: C  376 GLU cc_start: 0.7939 (tp30) cc_final: 0.7528 (tp30)
REVERT: C  397 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8601 (mp)
REVERT: D  145 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8271 (mt)
REVERT: D  376 GLU cc_start: 0.7973 (tp30) cc_final: 0.7580 (tp30)
REVERT: D  397 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8611 (mp)
  outliers start: 57
  outliers final: 39
  residues processed: 241
  average time/residue: 0.2251
  time to fit residues: 78.8702
Evaluate side-chains
  241 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 193
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  161 MET
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   72 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain C residue  397 LEU
Chi-restraints excluded: chain D residue   72 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  361 ILE
Chi-restraints excluded: chain D residue  397 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 102 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0050
   chunk 39 optimal weight:    0.6980
   chunk 122 optimal weight:    0.0470
   overall best weight:    0.7294

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

Flipped N/Q/H residues before XYZ refinement:
A 423 GLN
B 173 GLN
C 173 GLN
D   7 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.164994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.127343 restraints weight = 14286.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.17
r_work: 0.3318 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12304  Z= 0.115
  Angle     :  0.528   9.702  16660  Z= 0.260
  Chirality :  0.038   0.325   1984
  Planarity :  0.003   0.036   2008
  Dihedral  :  3.806  37.021   1738
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 28.56 %
    Favored  : 67.27 %
  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:  2.52 (0.22), residues: 1472
  helix:  2.48 (0.14), residues: 1228
  sheet: -1.42 (0.67), residues: 40
  loop : -3.06 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.010   0.001   PHE C 192 
 TYR   0.009   0.001   TYR B 214 
 ARG   0.002   0.000   ARG A 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  976)
  hydrogen bonds       : angle       3.45451 ( 2928)
  covalent geometry    : bond        0.00255 (12304)
  covalent geometry    : angle       0.52763 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 211
  time to evaluate  : 1.425 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.7022 (p0) cc_final: 0.6632 (m110)
REVERT: A  376 GLU cc_start: 0.7928 (tp30) cc_final: 0.7520 (tp30)
REVERT: A  384 GLN cc_start: 0.8702 (tt0) cc_final: 0.8464 (tt0)
REVERT: B  145 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8378 (mt)
REVERT: B  157 MET cc_start: 0.8500 (mtp) cc_final: 0.7761 (mtp)
REVERT: B  161 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.6023 (pmt)
REVERT: B  182 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8207 (m-80)
REVERT: B  376 GLU cc_start: 0.7946 (tp30) cc_final: 0.7521 (tp30)
REVERT: C  157 MET cc_start: 0.8483 (mtp) cc_final: 0.7711 (mtp)
REVERT: C  161 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.6011 (pmt)
REVERT: C  376 GLU cc_start: 0.7842 (tp30) cc_final: 0.7433 (tp30)
REVERT: D  145 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8309 (mt)
  outliers start: 55
  outliers final: 39
  residues processed: 251
  average time/residue: 0.2133
  time to fit residues: 79.4452
Evaluate side-chains
  246 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 202
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   72 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  161 MET
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   72 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain D residue    7 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   72 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  361 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 115 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 141 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 102 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 116 optimal weight:    0.8980
   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   7 ASN
A 423 GLN
B 173 GLN
C   7 ASN
D   7 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.164719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127266 restraints weight = 14326.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.16
r_work: 0.3285 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.194  12304  Z= 0.184
  Angle     :  0.794  59.196  16660  Z= 0.446
  Chirality :  0.043   0.346   1984
  Planarity :  0.003   0.062   2008
  Dihedral  :  3.852  36.984   1738
  Min Nonbonded Distance : 1.767

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 28.94 %
    Favored  : 67.27 %
  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:  2.47 (0.22), residues: 1472
  helix:  2.45 (0.14), residues: 1228
  sheet: -1.40 (0.67), residues: 40
  loop : -3.12 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 328 
 HIS   0.002   0.001   HIS D 189 
 PHE   0.010   0.001   PHE D 192 
 TYR   0.008   0.001   TYR B  96 
 ARG   0.002   0.000   ARG A 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  976)
  hydrogen bonds       : angle       3.47014 ( 2928)
  covalent geometry    : bond        0.00450 (12304)
  covalent geometry    : angle       0.79445 (16660)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 200
  time to evaluate  : 1.393 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.7027 (p0) cc_final: 0.6637 (m110)
REVERT: A  376 GLU cc_start: 0.7935 (tp30) cc_final: 0.7522 (tp30)
REVERT: A  384 GLN cc_start: 0.8698 (tt0) cc_final: 0.8461 (tt0)
REVERT: B  145 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8377 (mt)
REVERT: B  157 MET cc_start: 0.8507 (mtp) cc_final: 0.7764 (mtp)
REVERT: B  161 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6017 (pmt)
REVERT: B  182 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8221 (m-80)
REVERT: B  376 GLU cc_start: 0.7943 (tp30) cc_final: 0.7515 (tp30)
REVERT: C  157 MET cc_start: 0.8463 (mtp) cc_final: 0.7700 (mtp)
REVERT: C  161 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6003 (pmt)
REVERT: C  376 GLU cc_start: 0.7843 (tp30) cc_final: 0.7429 (tp30)
REVERT: D  145 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8316 (mt)
  outliers start: 50
  outliers final: 42
  residues processed: 236
  average time/residue: 0.2178
  time to fit residues: 75.7821
Evaluate side-chains
  247 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 200
  time to evaluate  : 1.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ASN
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue   72 LYS
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  102 LEU
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   72 LYS
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  161 MET
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  271 ILE
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  361 ILE
Chi-restraints excluded: chain C residue    7 ASN
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   72 LYS
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  161 MET
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  271 ILE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain D residue    7 ASN
Chi-restraints excluded: chain D residue   16 LEU
Chi-restraints excluded: chain D residue   72 LYS
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  145 ILE
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  296 VAL
Chi-restraints excluded: chain D residue  361 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 111 optimal weight:    9.9990
   chunk 147 optimal weight:    3.9990
   chunk 123 optimal weight:    0.5980
   chunk 105 optimal weight:    5.9990
   chunk 134 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 423 GLN
** D   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.164727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127319 restraints weight = 14315.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.16
r_work: 0.3251 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.194  12304  Z= 0.193
  Angle     :  0.641  25.060  16660  Z= 0.363
  Chirality :  0.042   0.346   1984
  Planarity :  0.004   0.093   2008
  Dihedral  :  3.852  36.984   1738
  Min Nonbonded Distance : 1.768

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 29.24 %
    Favored  : 67.20 %
  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:  2.47 (0.22), residues: 1472
  helix:  2.45 (0.14), residues: 1228
  sheet: -1.40 (0.67), residues: 40
  loop : -3.12 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 328 
 HIS   0.002   0.001   HIS D 189 
 PHE   0.010   0.001   PHE D 192 
 TYR   0.008   0.001   TYR B  96 
 ARG   0.002   0.000   ARG A 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03664 (  976)
  hydrogen bonds       : angle       3.47014 ( 2928)
  covalent geometry    : bond        0.00457 (12304)
  covalent geometry    : angle       0.64082 (16660)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5293.34 seconds
wall clock time: 92 minutes 3.74 seconds (5523.74 seconds total)