Starting phenix.real_space_refine
on Sat Jan 18 07:52:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_60022_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ze3_60022/01_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_60022/01_2025/8ze3_60022.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_60022.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ze3_60022/01_2025/8ze3_60022_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ze3_60022/01_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 6.79, per 1000 atoms: 0.56
  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: 2.81
  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: 0.97
  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: 3.58

  Time building geometry restraints manager: 3.25 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:             0.460
  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:             0.020
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.260
  Find NCS groups from input model:        0.240
  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:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.240
-------------------------------------------------------------------------------
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= 0.250
  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 

*********************** 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  : 1.249 
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: 0.2485
  time to fit residues: 101.9568
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  : 1.372 
-------------------------------------------------------------------------------
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 = 42)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.129497 restraints weight = 14278.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.17
r_work: 0.3269 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
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= 0.196
  Angle     :  0.512   7.847  16660  Z= 0.262
  Chirality :  0.037   0.224   1984
  Planarity :  0.003   0.026   2008
  Dihedral  :  7.245  58.034   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 

*********************** 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  : 1.734 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.7097 (p0) cc_final: 0.6777 (m-40)
REVERT: A  330 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.6836 (mp-120)
REVERT: B   93 THR cc_start: 0.8998 (m) cc_final: 0.8751 (m)
REVERT: B  145 ILE cc_start: 0.8390 (mp) cc_final: 0.8045 (mp)
REVERT: B  324 ASN cc_start: 0.7300 (p0) cc_final: 0.6825 (m-40)
REVERT: B  330 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7003 (mp-120)
REVERT: B  346 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8215 (tp30)
REVERT: C  324 ASN cc_start: 0.7061 (p0) cc_final: 0.6658 (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: 0.8277 (ttm170) cc_final: 0.7891 (ttm170)
REVERT: D  145 ILE cc_start: 0.8266 (mp) cc_final: 0.7913 (mp)
REVERT: D  324 ASN cc_start: 0.7083 (p0) cc_final: 0.6785 (m-40)
REVERT: D  330 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.6830 (mp-120)
  outliers start: 61
  outliers final: 34
  residues processed: 281
  average time/residue: 0.2324
  time to fit residues: 95.5228
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  : 1.306 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   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:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.165496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.126648 restraints weight = 14317.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 2.18
r_work: 0.3055 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12304  Z= 0.214
  Angle     :  0.503   7.573  16660  Z= 0.260
  Chirality :  0.036   0.134   1984
  Planarity :  0.003   0.025   2008
  Dihedral  :  4.991  42.275   1744
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 25.61 %
    Favored  : 69.39 %
  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:  2.13 (0.22), residues: 1472
  helix:  2.20 (0.14), residues: 1228
  sheet: -2.02 (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 B 328 
 HIS   0.004   0.001   HIS D 189 
 PHE   0.012   0.001   PHE C 192 
 TYR   0.014   0.001   TYR B 326 
 ARG   0.005   0.000   ARG D 367 

*********************** 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: 66
    poor density    : 229
  time to evaluate  : 1.438 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6989 (p0) cc_final: 0.6590 (m-40)
REVERT: A  330 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6600 (mp-120)
REVERT: B   22 TYR cc_start: 0.8395 (m-10) cc_final: 0.8127 (m-10)
REVERT: B   93 THR cc_start: 0.8926 (m) cc_final: 0.8722 (m)
REVERT: B  145 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7969 (mp)
REVERT: B  209 MET cc_start: 0.8295 (tpp) cc_final: 0.8072 (tpt)
REVERT: B  324 ASN cc_start: 0.7181 (p0) cc_final: 0.6635 (m-40)
REVERT: B  330 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6727 (mp-120)
REVERT: C   25 LYS cc_start: 0.7621 (mmmm) cc_final: 0.7348 (mmmm)
REVERT: C   33 GLU cc_start: 0.7795 (tt0) cc_final: 0.7329 (pt0)
REVERT: C  324 ASN cc_start: 0.6935 (p0) cc_final: 0.6466 (m-40)
REVERT: C  330 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6816 (mp-120)
REVERT: C  376 GLU cc_start: 0.8010 (tp30) cc_final: 0.7803 (tp30)
REVERT: D  116 ASP cc_start: 0.8286 (m-30) cc_final: 0.7959 (m-30)
REVERT: D  129 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7653 (ttm170)
REVERT: D  145 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7996 (mp)
REVERT: D  324 ASN cc_start: 0.6792 (p0) cc_final: 0.6444 (m-40)
REVERT: D  330 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.6788 (mp-120)
  outliers start: 66
  outliers final: 37
  residues processed: 273
  average time/residue: 0.2222
  time to fit residues: 89.4102
Evaluate side-chains
  246 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 203
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
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  283 LYS
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   71 MET
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  330 GLN
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:    3.9990
   chunk 143 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 145 optimal weight:    0.6980
   chunk 37 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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   7 ASN
B 173 GLN
B 330 GLN
C   7 ASN
C 173 GLN
C 330 GLN
D   7 ASN
D 330 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.155926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113889 restraints weight = 14116.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.27
r_work: 0.3126 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12304  Z= 0.369
  Angle     :  0.564   8.308  16660  Z= 0.295
  Chirality :  0.040   0.284   1984
  Planarity :  0.003   0.023   2008
  Dihedral  :  4.866  50.370   1744
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 25.08 %
    Favored  : 69.70 %
  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:  1.97 (0.21), residues: 1472
  helix:  2.09 (0.14), residues: 1228
  sheet: -1.85 (0.67), residues: 40
  loop : -3.07 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.016   0.002   PHE C 192 
 TYR   0.013   0.002   TYR D 214 
 ARG   0.005   0.000   ARG C 367 

*********************** 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
  278 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 209
  time to evaluate  : 1.334 
Fit side-chains
REVERT: A  209 MET cc_start: 0.8228 (tpp) cc_final: 0.7967 (tpt)
REVERT: A  324 ASN cc_start: 0.7011 (p0) cc_final: 0.6590 (m-40)
REVERT: A  330 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6656 (mp-120)
REVERT: B  145 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8253 (mt)
REVERT: B  182 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8340 (m-80)
REVERT: B  209 MET cc_start: 0.8418 (tpp) cc_final: 0.8211 (tpt)
REVERT: B  324 ASN cc_start: 0.7129 (p0) cc_final: 0.6670 (m-40)
REVERT: C  182 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (m-80)
REVERT: C  209 MET cc_start: 0.8489 (tpp) cc_final: 0.8285 (tpt)
REVERT: C  324 ASN cc_start: 0.6956 (p0) cc_final: 0.6420 (m-40)
REVERT: C  376 GLU cc_start: 0.7997 (tp30) cc_final: 0.7711 (tp30)
REVERT: D  129 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7758 (ttm170)
REVERT: D  145 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8282 (mt)
REVERT: D  209 MET cc_start: 0.8463 (tpp) cc_final: 0.8261 (tpt)
REVERT: D  324 ASN cc_start: 0.6943 (p0) cc_final: 0.6517 (m-40)
REVERT: D  330 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6786 (mp-120)
REVERT: D  376 GLU cc_start: 0.8017 (tp30) cc_final: 0.7737 (tp30)
  outliers start: 69
  outliers final: 41
  residues processed: 261
  average time/residue: 0.2246
  time to fit residues: 86.3489
Evaluate side-chains
  238 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 191
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
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  330 GLN
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   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   71 MET
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   86 VAL
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  330 GLN
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:    0.8980
   chunk 146 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 125 optimal weight:    0.6980
   chunk 142 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 127 optimal weight:   10.0000
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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   7 ASN
B 173 GLN
B 330 GLN
C   7 ASN
C 173 GLN
C 330 GLN
D   7 ASN
D 330 GLN
D 383 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.160756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118758 restraints weight = 14154.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.32
r_work: 0.3185 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2160

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= 0.179
  Angle     :  0.491   8.440  16660  Z= 0.252
  Chirality :  0.036   0.254   1984
  Planarity :  0.003   0.025   2008
  Dihedral  :  4.475  37.240   1742
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 26.67 %
    Favored  : 68.71 %
  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:  2.28 (0.21), residues: 1472
  helix:  2.31 (0.14), residues: 1228
  sheet: -1.86 (0.67), residues: 40
  loop : -3.02 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.009   0.001   PHE A 192 
 TYR   0.011   0.001   TYR D 214 
 ARG   0.004   0.000   ARG C 367 

*********************** 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
  281 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 220
  time to evaluate  : 1.336 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6985 (p0) cc_final: 0.6496 (m-40)
REVERT: A  330 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6728 (mp-120)
REVERT: A  376 GLU cc_start: 0.7985 (tp30) cc_final: 0.7626 (tp30)
REVERT: A  397 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8499 (mt)
REVERT: B  145 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8213 (mt)
REVERT: B  182 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8217 (m-80)
REVERT: B  324 ASN cc_start: 0.7046 (p0) cc_final: 0.6567 (m-40)
REVERT: B  397 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8462 (mt)
REVERT: C  376 GLU cc_start: 0.7946 (tp30) cc_final: 0.7596 (tp30)
REVERT: C  397 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8468 (mt)
REVERT: D  129 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7725 (ttm170)
REVERT: D  145 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8217 (mt)
REVERT: D  324 ASN cc_start: 0.6918 (p0) cc_final: 0.6464 (m-40)
REVERT: D  330 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6908 (mp-120)
REVERT: D  376 GLU cc_start: 0.8058 (tp30) cc_final: 0.7724 (tp30)
  outliers start: 61
  outliers final: 39
  residues processed: 263
  average time/residue: 0.2185
  time to fit residues: 84.6627
Evaluate side-chains
  241 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 194
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
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  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 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  296 VAL
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   60 LEU
Chi-restraints excluded: chain C residue   71 MET
Chi-restraints excluded: chain C residue   75 THR
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  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   60 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  296 VAL
Chi-restraints excluded: chain D residue  330 GLN
Chi-restraints excluded: chain D residue  361 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 121 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 142 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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   7 ASN
B 173 GLN
C   7 ASN
C 173 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 = 0.3817 r_free = 0.3817 target = 0.160478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118368 restraints weight = 14319.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.35
r_work: 0.3194 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12304  Z= 0.197
  Angle     :  0.500   8.681  16660  Z= 0.257
  Chirality :  0.037   0.224   1984
  Planarity :  0.003   0.025   2008
  Dihedral  :  4.282  36.914   1742
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 27.50 %
    Favored  : 67.80 %
  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 (0.21), residues: 1472
  helix:  2.38 (0.14), residues: 1228
  sheet: -1.77 (0.67), residues: 40
  loop : -3.04 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.011   0.001   PHE C 192 
 TYR   0.016   0.001   TYR D 326 
 ARG   0.003   0.000   ARG C 367 

*********************** 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
  277 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 215
  time to evaluate  : 1.349 
Fit side-chains
REVERT: A  209 MET cc_start: 0.8344 (tpp) cc_final: 0.8099 (tpt)
REVERT: A  324 ASN cc_start: 0.7037 (p0) cc_final: 0.6569 (m-40)
REVERT: A  376 GLU cc_start: 0.7941 (tp30) cc_final: 0.7567 (tp30)
REVERT: A  397 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8521 (mt)
REVERT: B  145 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8227 (mt)
REVERT: B  182 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8228 (m-80)
REVERT: B  324 ASN cc_start: 0.7004 (p0) cc_final: 0.6557 (m110)
REVERT: B  397 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8481 (mt)
REVERT: C  161 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5792 (pmt)
REVERT: C  376 GLU cc_start: 0.7968 (tp30) cc_final: 0.7594 (tp30)
REVERT: C  397 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8492 (mt)
REVERT: D   33 GLU cc_start: 0.7803 (tt0) cc_final: 0.7364 (pt0)
REVERT: D  129 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7779 (ttm170)
REVERT: D  145 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: D  157 MET cc_start: 0.8473 (mtp) cc_final: 0.8233 (mtp)
REVERT: D  376 GLU cc_start: 0.7982 (tp30) cc_final: 0.7613 (tp30)
REVERT: D  397 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8495 (mt)
  outliers start: 62
  outliers final: 40
  residues processed: 255
  average time/residue: 0.2259
  time to fit residues: 84.5144
Evaluate side-chains
  253 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 205
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
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  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    7 ASN
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  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   60 LEU
Chi-restraints excluded: chain C residue   71 MET
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  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   16 LEU
Chi-restraints excluded: chain D residue   60 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 143 optimal weight:    3.9990
   chunk 141 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   chunk 136 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 113 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 125 optimal weight:    0.7980
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 278 HIS
A 330 GLN
B   7 ASN
C 173 GLN
D 330 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.161021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.122681 restraints weight = 14395.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.18
r_work: 0.3157 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12304  Z= 0.295
  Angle     :  0.544   9.864  16660  Z= 0.279
  Chirality :  0.038   0.299   1984
  Planarity :  0.003   0.024   2008
  Dihedral  :  4.297  36.863   1742
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 27.42 %
    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:  2.30 (0.22), residues: 1472
  helix:  2.32 (0.14), residues: 1228
  sheet: -1.57 (0.68), residues: 40
  loop : -3.08 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.014   0.001   PHE C 192 
 TYR   0.010   0.001   TYR D 214 
 ARG   0.004   0.000   ARG C 367 

*********************** 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
  274 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 208
  time to evaluate  : 1.447 
Fit side-chains
REVERT: A  209 MET cc_start: 0.8311 (tpp) cc_final: 0.8107 (tpt)
REVERT: A  324 ASN cc_start: 0.6928 (p0) cc_final: 0.6567 (m-40)
REVERT: A  376 GLU cc_start: 0.7994 (tp30) cc_final: 0.7597 (tp30)
REVERT: B    7 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7794 (p0)
REVERT: B  145 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8365 (mt)
REVERT: B  182 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8462 (m-80)
REVERT: B  324 ASN cc_start: 0.7049 (p0) cc_final: 0.6652 (m-40)
REVERT: B  397 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8504 (mp)
REVERT: C  157 MET cc_start: 0.8447 (mtp) cc_final: 0.7734 (mtp)
REVERT: C  161 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5845 (pmt)
REVERT: C  182 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8409 (m-80)
REVERT: C  376 GLU cc_start: 0.7868 (tp30) cc_final: 0.7486 (tp30)
REVERT: D   33 GLU cc_start: 0.7837 (tt0) cc_final: 0.7406 (pt0)
REVERT: D  145 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8381 (mt)
REVERT: D  157 MET cc_start: 0.8581 (mtp) cc_final: 0.7712 (mtp)
REVERT: D  161 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5801 (pmt)
REVERT: D  376 GLU cc_start: 0.7923 (tp30) cc_final: 0.7558 (tp30)
  outliers start: 66
  outliers final: 45
  residues processed: 258
  average time/residue: 0.2389
  time to fit residues: 89.1243
Evaluate side-chains
  255 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 202
  time to evaluate  : 1.307 
-------------------------------------------------------------------------------
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  296 VAL
Chi-restraints excluded: chain A residue  361 ILE
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain B residue    7 ASN
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   91 ILE
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 B residue  397 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   71 MET
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  283 LYS
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  361 ILE
Chi-restraints excluded: chain D residue   60 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  161 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 108 optimal weight:    0.0570
   chunk 94 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 117 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   overall best weight:    1.6104

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.162220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.124241 restraints weight = 14414.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.19
r_work: 0.3010 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12304  Z= 0.234
  Angle     :  0.534   9.467  16660  Z= 0.268
  Chirality :  0.038   0.346   1984
  Planarity :  0.003   0.028   2008
  Dihedral  :  4.175  37.123   1742
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 27.65 %
    Favored  : 67.50 %
  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:  2.37 (0.22), residues: 1472
  helix:  2.37 (0.14), residues: 1228
  sheet: -1.55 (0.67), residues: 40
  loop : -3.11 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 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 

*********************** 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
  268 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 204
  time to evaluate  : 1.307 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6804 (p0) cc_final: 0.6372 (m-40)
REVERT: A  376 GLU cc_start: 0.8060 (tp30) cc_final: 0.7640 (tp30)
REVERT: A  397 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8573 (mp)
REVERT: B  145 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8256 (mt)
REVERT: B  157 MET cc_start: 0.8187 (mtp) cc_final: 0.7412 (mtp)
REVERT: B  161 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5815 (pmt)
REVERT: B  182 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8372 (m-80)
REVERT: B  324 ASN cc_start: 0.6863 (p0) cc_final: 0.6390 (m-40)
REVERT: B  397 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8570 (mp)
REVERT: C  161 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5837 (pmt)
REVERT: C  171 ASN cc_start: 0.7575 (t0) cc_final: 0.7373 (t0)
REVERT: C  182 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8329 (m-80)
REVERT: C  376 GLU cc_start: 0.7942 (tp30) cc_final: 0.7545 (tp30)
REVERT: D  145 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8271 (mt)
REVERT: D  157 MET cc_start: 0.8311 (mtp) cc_final: 0.7452 (mtp)
REVERT: D  161 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5816 (pmt)
REVERT: D  376 GLU cc_start: 0.7977 (tp30) cc_final: 0.7596 (tp30)
  outliers start: 64
  outliers final: 41
  residues processed: 253
  average time/residue: 0.2369
  time to fit residues: 86.9838
Evaluate side-chains
  249 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 199
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
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  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  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  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   60 LEU
Chi-restraints excluded: chain C residue   71 MET
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 D residue   16 LEU
Chi-restraints excluded: chain D residue   60 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  161 MET
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain D residue  271 ILE
Chi-restraints excluded: chain D residue  361 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 72 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 102 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0370
   chunk 39 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.9062

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

Flipped N/Q/H residues before XYZ refinement:
A 423 GLN
B   7 ASN
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 = 0.3905 r_free = 0.3905 target = 0.166693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.128992 restraints weight = 14323.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.18
r_work: 0.3063 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12304  Z= 0.176
  Angle     :  0.523   9.586  16660  Z= 0.260
  Chirality :  0.038   0.328   1984
  Planarity :  0.003   0.026   2008
  Dihedral  :  3.944  37.109   1741
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 28.56 %
    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:  2.52 (0.22), residues: 1472
  helix:  2.48 (0.14), residues: 1228
  sheet: -1.44 (0.66), residues: 40
  loop : -3.12 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.010   0.001   PHE D 192 
 TYR   0.009   0.001   TYR B 214 
 ARG   0.003   0.000   ARG C 367 

*********************** 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
  278 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 222
  time to evaluate  : 1.314 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6815 (p0) cc_final: 0.6334 (m110)
REVERT: A  376 GLU cc_start: 0.8050 (tp30) cc_final: 0.7632 (tp30)
REVERT: A  397 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8525 (mp)
REVERT: B  145 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8228 (mt)
REVERT: B  157 MET cc_start: 0.8183 (mtp) cc_final: 0.7386 (mtp)
REVERT: B  161 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.5818 (pmt)
REVERT: B  182 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8168 (m-80)
REVERT: B  324 ASN cc_start: 0.6815 (p0) cc_final: 0.6327 (m110)
REVERT: B  376 GLU cc_start: 0.8016 (tp30) cc_final: 0.7602 (tp30)
REVERT: B  397 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8547 (mt)
REVERT: C  157 MET cc_start: 0.8165 (mtp) cc_final: 0.7427 (mtp)
REVERT: C  161 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5883 (pmt)
REVERT: C  376 GLU cc_start: 0.7929 (tp30) cc_final: 0.7523 (tp30)
REVERT: D  145 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8143 (mt)
REVERT: D  157 MET cc_start: 0.8286 (mtp) cc_final: 0.7429 (mtp)
REVERT: D  376 GLU cc_start: 0.7947 (tp30) cc_final: 0.7554 (tp30)
  outliers start: 56
  outliers final: 39
  residues processed: 259
  average time/residue: 0.2207
  time to fit residues: 84.2613
Evaluate side-chains
  257 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 211
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
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  361 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue    7 ASN
Chi-restraints excluded: chain B residue   16 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  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  361 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   71 MET
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  271 ILE
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   60 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
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:    3.9990
   chunk 141 optimal weight:    3.9990
   chunk 118 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 80 optimal weight:    0.0980
   chunk 102 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 116 optimal weight:    0.9980
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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   7 ASN
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 = 0.3882 r_free = 0.3882 target = 0.164492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.126796 restraints weight = 14356.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.18
r_work: 0.3120 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.189  12304  Z= 0.323
  Angle     :  0.976  59.200  16660  Z= 0.577
  Chirality :  0.040   0.333   1984
  Planarity :  0.003   0.057   2008
  Dihedral  :  3.849  37.075   1738
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 29.24 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.49 (0.22), residues: 1472
  helix:  2.47 (0.14), residues: 1228
  sheet: -1.43 (0.66), residues: 40
  loop : -3.20 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.010   0.001   PHE D 192 
 TYR   0.008   0.001   TYR B 214 
 ARG   0.004   0.000   ARG B 367 

********************** 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
  260 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 208
  time to evaluate  : 1.384 
Fit side-chains
REVERT: A  324 ASN cc_start: 0.6805 (p0) cc_final: 0.6344 (m110)
REVERT: A  376 GLU cc_start: 0.8059 (tp30) cc_final: 0.7637 (tp30)
REVERT: A  397 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8551 (mp)
REVERT: B  145 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (mt)
REVERT: B  157 MET cc_start: 0.8176 (mtp) cc_final: 0.7383 (mtp)
REVERT: B  161 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5816 (pmt)
REVERT: B  182 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8185 (m-80)
REVERT: B  324 ASN cc_start: 0.6841 (p0) cc_final: 0.6354 (m110)
REVERT: B  376 GLU cc_start: 0.8021 (tp30) cc_final: 0.7603 (tp30)
REVERT: B  397 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (mt)
REVERT: C  157 MET cc_start: 0.8169 (mtp) cc_final: 0.7482 (mtp)
REVERT: C  161 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5879 (pmt)
REVERT: C  376 GLU cc_start: 0.7936 (tp30) cc_final: 0.7526 (tp30)
REVERT: D  145 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8157 (mt)
REVERT: D  157 MET cc_start: 0.7820 (mtp) cc_final: 0.7597 (mtp)
REVERT: D  376 GLU cc_start: 0.7948 (tp30) cc_final: 0.7559 (tp30)
  outliers start: 52
  outliers final: 41
  residues processed: 244
  average time/residue: 0.2321
  time to fit residues: 82.1626
Evaluate side-chains
  256 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 208
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
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  361 ILE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain B residue    7 ASN
Chi-restraints excluded: chain B residue   16 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   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  361 ILE
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   71 MET
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  271 ILE
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   60 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  283 LYS
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:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 134 optimal weight:    0.7980
   chunk 41 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 125 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   7 ASN
** D   7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.164483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.127000 restraints weight = 14325.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.16
r_work: 0.3051 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.189  12304  Z= 0.312
  Angle     :  0.861  58.623  16660  Z= 0.520
  Chirality :  0.040   0.333   1984
  Planarity :  0.004   0.108   2008
  Dihedral  :  3.849  37.075   1738
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 29.39 %
    Favored  : 66.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.49 (0.22), residues: 1472
  helix:  2.47 (0.14), residues: 1228
  sheet: -1.43 (0.66), residues: 40
  loop : -3.20 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 328 
 HIS   0.003   0.001   HIS D 189 
 PHE   0.010   0.001   PHE D 192 
 TYR   0.008   0.001   TYR B 214 
 ARG   0.004   0.000   ARG B 367 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4866.10 seconds
wall clock time: 87 minutes 48.82 seconds (5268.82 seconds total)