Starting phenix.real_space_refine
on Wed Mar 12 00:27:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g3g_29695/03_2025/8g3g_29695.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g3g_29695/03_2025/8g3g_29695.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2025/8g3g_29695.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2025/8g3g_29695.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2025/8g3g_29695.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g3g_29695/03_2025/8g3g_29695.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      10      5.16       5
     C    4400      2.51       5
     N    1280      2.21       5
     O    1330      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7020
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "J"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "A"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "B"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "C"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "D"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "E"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "F"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "G"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "H"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 702
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 1, 'TRANS': 88}
  Time building chain proxies: 4.71, per 1000 atoms: 0.67
  Number of scatterers: 7020
  At special positions: 0
  Unit cell: (89.3, 91.18, 62.98, 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      10     16.00
     O    1330      8.00
     N    1280      7.00
     C    4400      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: 1.56
  Conformation dependent library (CDL) restraints added in 937.7 milliseconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1620

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      35.3% alpha, 31.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'J' and resid 1 through 8
    Processing helix  chain 'J' and resid 73 through 86
    Processing helix  chain 'A' and resid 2 through 8
    Processing helix  chain 'A' and resid 65 through 86
      removed outlier: 4.418A  pdb=" N   ALA A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LYS A  72 " --> pdb=" O   PHE A  68 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 8
    Processing helix  chain 'B' and resid 27 through 31
    Processing helix  chain 'B' and resid 65 through 86
      removed outlier: 3.893A  pdb=" N   ARG B  70 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ALA B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LYS B  72 " --> pdb=" O   PHE B  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 8
    Processing helix  chain 'C' and resid 27 through 31
    Processing helix  chain 'C' and resid 65 through 86
      removed outlier: 3.585A  pdb=" N   ARG C  70 " --> pdb=" O   ALA C  66 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   ALA C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   LYS C  72 " --> pdb=" O   PHE C  68 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 8
    Processing helix  chain 'D' and resid 27 through 31
    Processing helix  chain 'D' and resid 65 through 86
      removed outlier: 3.810A  pdb=" N   ALA D  71 " --> pdb=" O   ALA D  67 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LYS D  72 " --> pdb=" O   PHE D  68 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 8
    Processing helix  chain 'E' and resid 27 through 31
    Processing helix  chain 'E' and resid 66 through 86
      removed outlier: 4.069A  pdb=" N   ARG E  70 " --> pdb=" O   ALA E  66 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ALA E  71 " --> pdb=" O   ALA E  67 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   LYS E  72 " --> pdb=" O   PHE E  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 8
    Processing helix  chain 'F' and resid 27 through 31
    Processing helix  chain 'F' and resid 65 through 86
      removed outlier: 3.633A  pdb=" N   ARG F  70 " --> pdb=" O   ALA F  66 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ALA F  71 " --> pdb=" O   ALA F  67 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   LYS F  72 " --> pdb=" O   PHE F  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 8
    Processing helix  chain 'G' and resid 27 through 31
    Processing helix  chain 'G' and resid 68 through 86
      removed outlier: 4.269A  pdb=" N   LYS G  72 " --> pdb=" O   PHE G  68 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 2 through 8
    Processing helix  chain 'H' and resid 27 through 31
    Processing helix  chain 'H' and resid 65 through 86
      removed outlier: 3.766A  pdb=" N   ARG H  70 " --> pdb=" O   ALA H  66 " (cutoff:3.500A)
      removed outlier: 4.743A  pdb=" N   ALA H  71 " --> pdb=" O   ALA H  67 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS H  72 " --> pdb=" O   PHE H  68 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 8
    Processing helix  chain 'I' and resid 27 through 31
    Processing helix  chain 'I' and resid 65 through 71
      removed outlier: 3.718A  pdb=" N   ARG I  70 " --> pdb=" O   ALA I  66 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA I  71 " --> pdb=" O   ALA I  67 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 72 through 86
    Processing sheet with id=AA1, first strand: chain 'J' and resid 15 through 22
      removed outlier: 5.911A  pdb=" N   THR J  15 " --> pdb=" O   THR J  43 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   THR J  43 " --> pdb=" O   THR J  15 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   VAL J  17 " --> pdb=" O   ARG J  41 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ARG J  41 " --> pdb=" O   VAL J  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 15 through 22
      removed outlier: 5.911A  pdb=" N   THR J  15 " --> pdb=" O   THR J  43 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   THR J  43 " --> pdb=" O   THR J  15 " (cutoff:3.500A)
      removed outlier: 5.319A  pdb=" N   VAL J  17 " --> pdb=" O   ARG J  41 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ARG J  41 " --> pdb=" O   VAL J  17 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 24
      removed outlier: 6.752A  pdb=" N   ILE A  39 " --> pdb=" O   LYS A  18 " (cutoff:3.500A)
      removed outlier: 4.280A  pdb=" N   VAL A  20 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   THR A  37 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ILE A  22 " --> pdb=" O   GLY A  35 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   GLY A  35 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 22
      removed outlier: 6.644A  pdb=" N   ILE B  39 " --> pdb=" O   LYS B  18 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL B  20 " --> pdb=" O   THR B  37 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   THR B  37 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 5.221A  pdb=" N   ILE B  22 " --> pdb=" O   GLY B  35 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   GLY B  35 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL B  40 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 22
    Processing sheet with id=AA6, first strand: chain 'D' and resid 17 through 22
      removed outlier: 6.324A  pdb=" N   VAL D  17 " --> pdb=" O   ARG D  41 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ARG D  41 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL D  42 " --> pdb=" O   ARG D  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 22
      removed outlier: 6.324A  pdb=" N   VAL D  17 " --> pdb=" O   ARG D  41 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ARG D  41 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 17 through 25
      removed outlier: 5.957A  pdb=" N   VAL E  17 " --> pdb=" O   ARG E  41 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   ARG E  41 " --> pdb=" O   VAL E  17 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   SER E  19 " --> pdb=" O   ILE E  39 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ASP E  23 " --> pdb=" O   GLY E  35 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   GLY E  35 " --> pdb=" O   ASP E  23 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL E  40 " --> pdb=" O   ASP E  52 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 14 through 22
      removed outlier: 5.515A  pdb=" N   THR F  15 " --> pdb=" O   THR F  43 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   THR F  43 " --> pdb=" O   THR F  15 " (cutoff:3.500A)
      removed outlier: 5.637A  pdb=" N   VAL F  17 " --> pdb=" O   ARG F  41 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   ARG F  41 " --> pdb=" O   VAL F  17 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL F  40 " --> pdb=" O   ASP F  52 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ASP F  52 " --> pdb=" O   VAL F  40 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL F  42 " --> pdb=" O   ARG F  50 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'G' and resid 16 through 22
      removed outlier: 5.383A  pdb=" N   VAL G  17 " --> pdb=" O   ARG G  41 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ARG G  41 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL G  42 " --> pdb=" O   ARG G  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 22
      removed outlier: 5.383A  pdb=" N   VAL G  17 " --> pdb=" O   ARG G  41 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   ARG G  41 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 14 through 24
      removed outlier: 5.632A  pdb=" N   THR H  15 " --> pdb=" O   THR H  43 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   THR H  43 " --> pdb=" O   THR H  15 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   VAL H  17 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG H  41 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   GLY H  35 " --> pdb=" O   ASP H  23 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL H  42 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 14 through 24
      removed outlier: 5.632A  pdb=" N   THR H  15 " --> pdb=" O   THR H  43 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   THR H  43 " --> pdb=" O   THR H  15 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   VAL H  17 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG H  41 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   GLY H  35 " --> pdb=" O   ASP H  23 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'I' and resid 16 through 22
      removed outlier: 5.276A  pdb=" N   VAL I  17 " --> pdb=" O   ARG I  41 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ARG I  41 " --> pdb=" O   VAL I  17 " (cutoff:3.500A)

    315 hydrogen bonds defined for protein.
    849 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.64

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1895
        1.33 -     1.45: 1307
        1.45 -     1.57: 3908
        1.57 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 7120
  Sorted by residual:
  bond pdb=" N   VAL B  21 "
       pdb=" CA  VAL B  21 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.042 1.14e-02 7.69e+03 1.38e+01
  bond pdb=" N   VAL D  40 "
       pdb=" CA  VAL D  40 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.040 1.11e-02 8.12e+03 1.28e+01
  bond pdb=" N   ILE H  22 "
       pdb=" CA  ILE H  22 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.26e-02 6.30e+03 1.10e+01
  bond pdb=" N   ILE A  34 "
       pdb=" CA  ILE A  34 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.15e-02 7.56e+03 1.08e+01
  bond pdb=" N   VAL H  40 "
       pdb=" CA  VAL H  40 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.037 1.14e-02 7.69e+03 1.07e+01
  ... (remaining 7115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 8953
        2.36 -     4.71: 548
        4.71 -     7.07: 63
        7.07 -     9.43: 3
        9.43 -    11.79: 3
  Bond angle restraints: 9570
  Sorted by residual:
  angle pdb=" CA  PHE J  68 "
        pdb=" CB  PHE J  68 "
        pdb=" CG  PHE J  68 "
      ideal   model   delta    sigma   weight residual
     113.80  120.25   -6.45 1.00e+00 1.00e+00 4.17e+01
  angle pdb=" N   ARG E  63 "
        pdb=" CA  ARG E  63 "
        pdb=" C   ARG E  63 "
      ideal   model   delta    sigma   weight residual
     109.96  100.39    9.57 1.50e+00 4.44e-01 4.07e+01
  angle pdb=" N   ALA E  66 "
        pdb=" CA  ALA E  66 "
        pdb=" C   ALA E  66 "
      ideal   model   delta    sigma   weight residual
     113.01  106.17    6.84 1.20e+00 6.94e-01 3.25e+01
  angle pdb=" C   GLN D  29 "
        pdb=" CA  GLN D  29 "
        pdb=" CB  GLN D  29 "
      ideal   model   delta    sigma   weight residual
     111.73  119.71   -7.98 1.42e+00 4.96e-01 3.16e+01
  angle pdb=" N   GLY D   9 "
        pdb=" CA  GLY D   9 "
        pdb=" C   GLY D   9 "
      ideal   model   delta    sigma   weight residual
     112.89  104.14    8.75 1.58e+00 4.01e-01 3.07e+01
  ... (remaining 9565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.70: 3456
       16.70 -    33.40: 564
       33.40 -    50.10: 154
       50.10 -    66.80: 45
       66.80 -    83.50: 21
  Dihedral angle restraints: 4240
    sinusoidal: 1700
      harmonic: 2540
  Sorted by residual:
  dihedral pdb=" C   GLN D  29 "
           pdb=" N   GLN D  29 "
           pdb=" CA  GLN D  29 "
           pdb=" CB  GLN D  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.76   14.16     0      2.50e+00 1.60e-01 3.21e+01
  dihedral pdb=" CA  LYS G  64 "
           pdb=" C   LYS G  64 "
           pdb=" N   PRO G  65 "
           pdb=" CA  PRO G  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.76   24.24     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  LYS B  64 "
           pdb=" C   LYS B  64 "
           pdb=" N   PRO B  65 "
           pdb=" CA  PRO B  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.26   23.74     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 4237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 834
       0.082 -    0.165: 166
       0.165 -    0.247: 46
       0.247 -    0.329: 11
       0.329 -    0.412: 3
  Chirality restraints: 1060
  Sorted by residual:
  chirality pdb=" CA  GLN D  29 "
            pdb=" N   GLN D  29 "
            pdb=" C   GLN D  29 "
            pdb=" CB  GLN D  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.24e+00
  chirality pdb=" CA  ILE H  39 "
            pdb=" N   ILE H  39 "
            pdb=" C   ILE H  39 "
            pdb=" CB  ILE H  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.81   -0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" CA  ARG E  63 "
            pdb=" N   ARG E  63 "
            pdb=" C   ARG E  63 "
            pdb=" CB  ARG E  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.77e+00
  ... (remaining 1057 not shown)

  Planarity restraints: 1240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E  33 "    0.014 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" C   SER E  33 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   SER E  33 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ILE E  34 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H  33 "   -0.012 2.00e-02 2.50e+03   2.47e-02 6.12e+00
        pdb=" C   SER H  33 "    0.043 2.00e-02 2.50e+03
        pdb=" O   SER H  33 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE H  34 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E  60 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.52e+00
        pdb=" C   ASN E  60 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASN E  60 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU E  61 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1237 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 950
        2.75 -     3.29: 7082
        3.29 -     3.83: 11790
        3.83 -     4.36: 14493
        4.36 -     4.90: 23163
  Nonbonded interactions: 57478
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG I  28 "
            pdb=" OE1 GLN I  29 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OD2 ASP C  23 "
            pdb=" OH  TYR C  55 "
     model   vdw
     2.403 3.040
  nonbonded pdb=" N   ASP D  52 "
            pdb=" OD1 ASP D  52 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" N   ASP H  52 "
            pdb=" OD1 ASP H  52 "
     model   vdw
     2.408 3.120
  nonbonded pdb=" N   ASP C  23 "
            pdb=" OD1 ASP C  23 "
     model   vdw
     2.432 3.120
  ... (remaining 57473 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.190
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   7120  Z= 0.448
  Angle     :  1.147  11.787   9570  Z= 0.763
  Chirality :  0.076   0.412   1060
  Planarity :  0.005   0.037   1240
  Dihedral  : 19.088  83.499   2620
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  9.45 %
    Allowed  : 29.59 %
    Favored  : 60.96 %
  Cbeta Deviations :  0.25 %
  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: -2.51 (0.27), residues: 880
  helix:  0.24 (0.33), residues: 210
  sheet: -2.10 (0.29), residues: 300
  loop : -2.31 (0.30), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  13 
 PHE   0.024   0.002   PHE J  68 
 TYR   0.016   0.002   TYR H  49 
 ARG   0.009   0.001   ARG F  62 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 260
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 TRP cc_start: 0.8083 (p-90) cc_final: 0.7707 (p-90)
REVERT: C   13 TRP cc_start: 0.8305 (p-90) cc_final: 0.7693 (p-90)
REVERT: E   23 ASP cc_start: 0.6412 (p0) cc_final: 0.6178 (p0)
REVERT: E   55 TYR cc_start: 0.7529 (t80) cc_final: 0.7267 (t80)
REVERT: E   68 PHE cc_start: 0.7012 (t80) cc_final: 0.6777 (t80)
REVERT: F   19 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8262 (p)
REVERT: G   49 TYR cc_start: 0.8247 (p90) cc_final: 0.7811 (p90)
REVERT: H   49 TYR cc_start: 0.8209 (p90) cc_final: 0.7904 (p90)
REVERT: I   19 SER cc_start: 0.8169 (OUTLIER) cc_final: 0.7784 (p)
  outliers start: 69
  outliers final: 16
  residues processed: 292
  average time/residue: 0.2885
  time to fit residues: 101.1467
Evaluate side-chains
  255 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 237
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   76 VAL
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   36 CYS
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain H residue   23 ASP
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain I residue   21 VAL
Chi-restraints excluded: chain I residue   48 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.152408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.130782 restraints weight = 11465.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.134217 restraints weight = 7307.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.136305 restraints weight = 5343.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7120  Z= 0.236
  Angle     :  0.717   6.423   9570  Z= 0.385
  Chirality :  0.047   0.207   1060
  Planarity :  0.004   0.032   1240
  Dihedral  :  7.040  54.337   1027
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.61 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  9.04 %
    Allowed  : 27.12 %
    Favored  : 63.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.27), residues: 880
  helix:  0.10 (0.32), residues: 210
  sheet: -1.88 (0.29), residues: 300
  loop : -2.16 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  13 
 PHE   0.016   0.001   PHE G  24 
 TYR   0.011   0.001   TYR B  49 
 ARG   0.011   0.001   ARG B  41 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 239
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J    6 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7977 (tm-30)
REVERT: J   41 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7965 (ttt90)
REVERT: J   68 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6219 (t80)
REVERT: E   68 PHE cc_start: 0.7446 (t80) cc_final: 0.7208 (t80)
REVERT: F   41 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8240 (ttm-80)
REVERT: G   31 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8296 (mmmt)
REVERT: G   41 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7671 (ttt90)
REVERT: I   19 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.7960 (p)
REVERT: I   28 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8494 (mmm160)
  outliers start: 66
  outliers final: 44
  residues processed: 270
  average time/residue: 0.2820
  time to fit residues: 91.5487
Evaluate side-chains
  269 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 220
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   23 ASP
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   41 ARG
Chi-restraints excluded: chain J residue   57 THR
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   76 VAL
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain A residue   33 SER
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   36 CYS
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   11 ASN
Chi-restraints excluded: chain G residue   21 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   41 ARG
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain I residue   23 ASP
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   48 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    2.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.140858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.118453 restraints weight = 11831.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.121423 restraints weight = 7901.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.123678 restraints weight = 6000.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.3284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.060   7120  Z= 0.574
  Angle     :  0.901   7.117   9570  Z= 0.493
  Chirality :  0.054   0.200   1060
  Planarity :  0.007   0.085   1240
  Dihedral  :  7.299  58.636   1018
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 17.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.89 %
    Favored  : 90.11 %
  Rotamer:
    Outliers : 13.29 %
    Allowed  : 24.79 %
    Favored  : 61.92 %
  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: -2.78 (0.26), residues: 880
  helix: -0.74 (0.31), residues: 200
  sheet: -1.89 (0.29), residues: 300
  loop : -2.30 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP I  13 
 PHE   0.037   0.003   PHE A  68 
 TYR   0.018   0.002   TYR B  55 
 ARG   0.010   0.001   ARG A  50 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 235
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   68 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5844 (t80)
REVERT: B   13 TRP cc_start: 0.8340 (p-90) cc_final: 0.7758 (p-90)
REVERT: C   41 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8298 (ttt90)
REVERT: C   49 TYR cc_start: 0.8233 (p90) cc_final: 0.7544 (p90)
REVERT: D   49 TYR cc_start: 0.8757 (p90) cc_final: 0.8390 (p90)
REVERT: E   68 PHE cc_start: 0.7672 (t80) cc_final: 0.7471 (t80)
REVERT: F    8 PHE cc_start: 0.8289 (m-10) cc_final: 0.8074 (m-10)
REVERT: F   41 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8522 (ttm-80)
REVERT: G   27 GLU cc_start: 0.8156 (tp30) cc_final: 0.7844 (tp30)
REVERT: H   13 TRP cc_start: 0.8285 (p-90) cc_final: 0.8011 (p-90)
REVERT: H   68 PHE cc_start: 0.7554 (t80) cc_final: 0.7258 (t80)
REVERT: I   49 TYR cc_start: 0.8844 (p90) cc_final: 0.8594 (p90)
  outliers start: 97
  outliers final: 84
  residues processed: 301
  average time/residue: 0.2646
  time to fit residues: 97.2802
Evaluate side-chains
  308 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 221
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   11 ASN
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   23 ASP
Chi-restraints excluded: chain J residue   34 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   41 ARG
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   45 THR
Chi-restraints excluded: chain J residue   53 ILE
Chi-restraints excluded: chain J residue   57 THR
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   83 SER
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   11 ASN
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   23 ASP
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   11 ASN
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   37 THR
Chi-restraints excluded: chain C residue   41 ARG
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   11 ASN
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   41 ARG
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain D residue   87 PHE
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   36 CYS
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   53 ILE
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   83 SER
Chi-restraints excluded: chain E residue   87 PHE
Chi-restraints excluded: chain F residue    1 ILE
Chi-restraints excluded: chain F residue   11 ASN
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   36 CYS
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain F residue   87 PHE
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   11 ASN
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   37 THR
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   87 PHE
Chi-restraints excluded: chain H residue    1 ILE
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   83 SER
Chi-restraints excluded: chain H residue   87 PHE
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   11 ASN
Chi-restraints excluded: chain I residue   19 SER
Chi-restraints excluded: chain I residue   21 VAL
Chi-restraints excluded: chain I residue   23 ASP
Chi-restraints excluded: chain I residue   34 ILE
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   42 VAL
Chi-restraints excluded: chain I residue   48 THR
Chi-restraints excluded: chain I residue   57 THR
Chi-restraints excluded: chain I residue   80 LEU
Chi-restraints excluded: chain I residue   87 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 89 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 42 optimal weight:    0.4980
   chunk 69 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.148044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.126056 restraints weight = 11529.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.129241 restraints weight = 7367.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.131737 restraints weight = 5445.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7120  Z= 0.212
  Angle     :  0.717   8.315   9570  Z= 0.381
  Chirality :  0.046   0.160   1060
  Planarity :  0.004   0.035   1240
  Dihedral  :  6.830  59.032   1014
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  7.95 %
    Allowed  : 30.96 %
    Favored  : 61.10 %
  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: -2.40 (0.27), residues: 880
  helix:  0.09 (0.32), residues: 200
  sheet: -1.94 (0.29), residues: 300
  loop : -2.12 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP I  13 
 PHE   0.013   0.001   PHE A  68 
 TYR   0.007   0.001   TYR C  49 
 ARG   0.006   0.001   ARG B  28 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 252
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   68 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.5859 (t80)
REVERT: B   13 TRP cc_start: 0.8340 (p-90) cc_final: 0.8056 (p-90)
REVERT: D   49 TYR cc_start: 0.8788 (p90) cc_final: 0.8484 (p90)
REVERT: E   14 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7921 (m)
REVERT: E   68 PHE cc_start: 0.7710 (t80) cc_final: 0.7499 (t80)
REVERT: F    8 PHE cc_start: 0.8292 (m-10) cc_final: 0.8036 (m-10)
REVERT: G   23 ASP cc_start: 0.7585 (p0) cc_final: 0.7158 (p0)
REVERT: G   27 GLU cc_start: 0.8177 (tp30) cc_final: 0.7943 (tp30)
REVERT: G   41 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8006 (ttt180)
REVERT: H   13 TRP cc_start: 0.8250 (p-90) cc_final: 0.8017 (p-90)
REVERT: I   19 SER cc_start: 0.8445 (p) cc_final: 0.8214 (p)
REVERT: I   73 LYS cc_start: 0.7094 (pttm) cc_final: 0.6813 (pttm)
  outliers start: 58
  outliers final: 44
  residues processed: 279
  average time/residue: 0.2881
  time to fit residues: 96.6005
Evaluate side-chains
  274 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 228
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain E residue   36 CYS
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   87 PHE
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   37 THR
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   87 PHE
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   48 THR
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   80 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.144533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.121640 restraints weight = 11675.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.125274 restraints weight = 7221.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.127257 restraints weight = 5191.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7120  Z= 0.290
  Angle     :  0.726   7.775   9570  Z= 0.389
  Chirality :  0.046   0.156   1060
  Planarity :  0.004   0.037   1240
  Dihedral  :  6.283  58.699   1011
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers : 10.82 %
    Allowed  : 29.59 %
    Favored  : 59.59 %
  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: -2.45 (0.27), residues: 880
  helix:  0.05 (0.33), residues: 200
  sheet: -1.99 (0.29), residues: 300
  loop : -2.14 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP I  13 
 PHE   0.019   0.002   PHE D  68 
 TYR   0.011   0.001   TYR E  49 
 ARG   0.005   0.001   ARG H  62 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 235
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   41 ARG cc_start: 0.8494 (ttt180) cc_final: 0.8121 (ttt90)
REVERT: J   68 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.5823 (t80)
REVERT: A   52 ASP cc_start: 0.6448 (OUTLIER) cc_final: 0.6119 (p0)
REVERT: B   13 TRP cc_start: 0.8454 (p-90) cc_final: 0.8105 (p-90)
REVERT: C   73 LYS cc_start: 0.7474 (pttp) cc_final: 0.7120 (pttp)
REVERT: D   27 GLU cc_start: 0.8308 (tp30) cc_final: 0.8022 (tp30)
REVERT: D   28 ARG cc_start: 0.8425 (mmm160) cc_final: 0.8016 (mmm160)
REVERT: D   29 GLN cc_start: 0.7368 (pm20) cc_final: 0.7088 (pm20)
REVERT: D   49 TYR cc_start: 0.8831 (p90) cc_final: 0.8589 (p90)
REVERT: E   14 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7963 (m)
REVERT: E   68 PHE cc_start: 0.7766 (t80) cc_final: 0.7412 (t80)
REVERT: F    8 PHE cc_start: 0.8414 (m-10) cc_final: 0.8172 (m-10)
REVERT: F   28 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8537 (mmm-85)
REVERT: G   27 GLU cc_start: 0.8185 (tp30) cc_final: 0.7797 (tp30)
REVERT: H   13 TRP cc_start: 0.8384 (p-90) cc_final: 0.8075 (p-90)
REVERT: H   68 PHE cc_start: 0.7510 (t80) cc_final: 0.7243 (t80)
REVERT: I   19 SER cc_start: 0.8556 (p) cc_final: 0.8326 (p)
REVERT: I   49 TYR cc_start: 0.8866 (p90) cc_final: 0.8543 (p90)
REVERT: I   73 LYS cc_start: 0.7226 (pttm) cc_final: 0.6974 (pttm)
  outliers start: 79
  outliers final: 70
  residues processed: 280
  average time/residue: 0.2834
  time to fit residues: 95.8130
Evaluate side-chains
  303 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 230
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   11 ASN
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   34 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   52 ASP
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   36 CYS
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   87 PHE
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   11 ASN
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   36 CYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   41 ARG
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   14 SER
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   62 ARG
Chi-restraints excluded: chain E residue   87 PHE
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   11 ASN
Chi-restraints excluded: chain G residue   21 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   37 THR
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   74 SER
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain H residue    1 ILE
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   87 PHE
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   11 ASN
Chi-restraints excluded: chain I residue   34 ILE
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   42 VAL
Chi-restraints excluded: chain I residue   48 THR
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   80 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 18 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.146884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.124916 restraints weight = 11632.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.128312 restraints weight = 7396.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.130227 restraints weight = 5411.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7120  Z= 0.224
  Angle     :  0.704   8.066   9570  Z= 0.374
  Chirality :  0.045   0.151   1060
  Planarity :  0.004   0.035   1240
  Dihedral  :  6.173  59.245   1010
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  9.18 %
    Allowed  : 30.68 %
    Favored  : 60.14 %
  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: -2.40 (0.27), residues: 880
  helix:  0.20 (0.33), residues: 200
  sheet: -2.02 (0.28), residues: 300
  loop : -2.10 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP I  13 
 PHE   0.012   0.001   PHE A  68 
 TYR   0.010   0.001   TYR I  55 
 ARG   0.007   0.001   ARG J  62 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 243
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   41 ARG cc_start: 0.8451 (ttt180) cc_final: 0.8062 (ttt90)
REVERT: J   68 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.5825 (t80)
REVERT: C   73 LYS cc_start: 0.7480 (pttp) cc_final: 0.7054 (pttp)
REVERT: D   27 GLU cc_start: 0.8243 (tp30) cc_final: 0.7944 (tp30)
REVERT: D   28 ARG cc_start: 0.8450 (mmm160) cc_final: 0.7951 (mmm160)
REVERT: D   29 GLN cc_start: 0.7373 (pm20) cc_final: 0.6836 (pm20)
REVERT: D   49 TYR cc_start: 0.8792 (p90) cc_final: 0.8527 (p90)
REVERT: E   68 PHE cc_start: 0.7737 (t80) cc_final: 0.7417 (t80)
REVERT: E   70 ARG cc_start: 0.5955 (ppt170) cc_final: 0.5475 (ppt170)
REVERT: F    8 PHE cc_start: 0.8409 (m-10) cc_final: 0.8116 (m-10)
REVERT: F   41 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8355 (ttt180)
REVERT: G   27 GLU cc_start: 0.8183 (tp30) cc_final: 0.7738 (tp30)
REVERT: G   41 ARG cc_start: 0.8387 (ttt180) cc_final: 0.7915 (ttt90)
REVERT: H   13 TRP cc_start: 0.8356 (p-90) cc_final: 0.8079 (p-90)
REVERT: I   19 SER cc_start: 0.8543 (p) cc_final: 0.8319 (p)
REVERT: I   28 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.8312 (mmm160)
  outliers start: 67
  outliers final: 59
  residues processed: 276
  average time/residue: 0.2951
  time to fit residues: 97.7939
Evaluate side-chains
  290 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 229
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   11 ASN
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   34 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   36 CYS
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   36 CYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   41 ARG
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   87 PHE
Chi-restraints excluded: chain F residue   11 ASN
Chi-restraints excluded: chain F residue   41 ARG
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   21 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   37 THR
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue   87 PHE
Chi-restraints excluded: chain H residue    1 ILE
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   11 ASN
Chi-restraints excluded: chain I residue   34 ILE
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   48 THR
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   57 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.146680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.124806 restraints weight = 11646.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.128180 restraints weight = 7468.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.130112 restraints weight = 5494.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7120  Z= 0.242
  Angle     :  0.723   8.012   9570  Z= 0.384
  Chirality :  0.045   0.235   1060
  Planarity :  0.004   0.033   1240
  Dihedral  :  6.063  59.370   1010
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers : 10.41 %
    Allowed  : 29.86 %
    Favored  : 59.73 %
  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: -2.39 (0.27), residues: 880
  helix:  0.27 (0.33), residues: 200
  sheet: -2.08 (0.28), residues: 300
  loop : -2.08 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B  13 
 PHE   0.026   0.001   PHE D  68 
 TYR   0.012   0.001   TYR E  49 
 ARG   0.006   0.001   ARG F  62 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 234
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   41 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8054 (ttt90)
REVERT: J   68 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5732 (t80)
REVERT: A   41 ARG cc_start: 0.8443 (ttt90) cc_final: 0.8159 (ttt90)
REVERT: C   73 LYS cc_start: 0.7561 (pttp) cc_final: 0.7316 (pttm)
REVERT: D   27 GLU cc_start: 0.8267 (tp30) cc_final: 0.7970 (tp30)
REVERT: D   28 ARG cc_start: 0.8466 (mmm160) cc_final: 0.7800 (mmm160)
REVERT: D   29 GLN cc_start: 0.7425 (pm20) cc_final: 0.6692 (pm20)
REVERT: D   49 TYR cc_start: 0.8790 (p90) cc_final: 0.8155 (p90)
REVERT: E   68 PHE cc_start: 0.7762 (t80) cc_final: 0.7363 (t80)
REVERT: F    8 PHE cc_start: 0.8402 (m-10) cc_final: 0.8181 (m-10)
REVERT: G   27 GLU cc_start: 0.8222 (tp30) cc_final: 0.7778 (tp30)
REVERT: G   31 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8098 (mmmt)
REVERT: G   41 ARG cc_start: 0.8386 (ttt180) cc_final: 0.7919 (ttt90)
REVERT: H   13 TRP cc_start: 0.8360 (p-90) cc_final: 0.8103 (p-90)
REVERT: I   19 SER cc_start: 0.8561 (p) cc_final: 0.8352 (p)
REVERT: I   28 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8130 (mmm160)
  outliers start: 76
  outliers final: 71
  residues processed: 275
  average time/residue: 0.2818
  time to fit residues: 93.7132
Evaluate side-chains
  302 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 230
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   11 ASN
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   34 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   57 THR
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   87 PHE
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   19 SER
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   36 CYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   41 ARG
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   87 PHE
Chi-restraints excluded: chain F residue   11 ASN
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   21 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   37 THR
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue   87 PHE
Chi-restraints excluded: chain H residue    1 ILE
Chi-restraints excluded: chain H residue   25 LEU
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   87 PHE
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   11 ASN
Chi-restraints excluded: chain I residue   34 ILE
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   42 VAL
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   57 THR
Chi-restraints excluded: chain I residue   80 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 88 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.146756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.124107 restraints weight = 11773.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.127695 restraints weight = 7358.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.129628 restraints weight = 5313.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7120  Z= 0.249
  Angle     :  0.741   9.048   9570  Z= 0.392
  Chirality :  0.045   0.206   1060
  Planarity :  0.004   0.033   1240
  Dihedral  :  5.770  59.910   1005
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers : 11.10 %
    Allowed  : 29.32 %
    Favored  : 59.59 %
  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: -2.39 (0.27), residues: 880
  helix:  0.30 (0.34), residues: 200
  sheet: -2.17 (0.28), residues: 300
  loop : -2.01 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  13 
 PHE   0.014   0.001   PHE I  24 
 TYR   0.010   0.001   TYR B  49 
 ARG   0.009   0.001   ARG G  62 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 234
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   41 ARG cc_start: 0.8427 (ttt180) cc_final: 0.8045 (ttt90)
REVERT: J   68 PHE cc_start: 0.6259 (OUTLIER) cc_final: 0.5727 (t80)
REVERT: A   41 ARG cc_start: 0.8425 (ttt90) cc_final: 0.8146 (ttt90)
REVERT: B   28 ARG cc_start: 0.8370 (mmm160) cc_final: 0.8074 (mmm-85)
REVERT: B   70 ARG cc_start: 0.5957 (ppt170) cc_final: 0.5467 (ppt170)
REVERT: C   29 GLN cc_start: 0.8050 (pm20) cc_final: 0.7834 (pm20)
REVERT: C   73 LYS cc_start: 0.7708 (pttp) cc_final: 0.7349 (pttm)
REVERT: D   27 GLU cc_start: 0.8284 (tp30) cc_final: 0.7991 (tp30)
REVERT: D   28 ARG cc_start: 0.8475 (mmm160) cc_final: 0.7804 (mmm160)
REVERT: D   29 GLN cc_start: 0.7470 (pm20) cc_final: 0.6686 (pm20)
REVERT: D   49 TYR cc_start: 0.8735 (p90) cc_final: 0.8120 (p90)
REVERT: E   68 PHE cc_start: 0.7828 (t80) cc_final: 0.7505 (t80)
REVERT: G   27 GLU cc_start: 0.8206 (tp30) cc_final: 0.7779 (tp30)
REVERT: H   13 TRP cc_start: 0.8361 (p-90) cc_final: 0.8116 (p-90)
  outliers start: 81
  outliers final: 76
  residues processed: 281
  average time/residue: 0.2887
  time to fit residues: 97.6468
Evaluate side-chains
  306 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 229
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   11 ASN
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   34 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   74 SER
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   87 PHE
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   11 ASN
Chi-restraints excluded: chain D residue   19 SER
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   36 CYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   41 ARG
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   87 PHE
Chi-restraints excluded: chain F residue   11 ASN
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain F residue   87 PHE
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   11 ASN
Chi-restraints excluded: chain G residue   21 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   37 THR
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue   87 PHE
Chi-restraints excluded: chain H residue    1 ILE
Chi-restraints excluded: chain H residue   25 LEU
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   87 PHE
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   11 ASN
Chi-restraints excluded: chain I residue   34 ILE
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   42 VAL
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   57 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.146986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.124450 restraints weight = 11834.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.128090 restraints weight = 7281.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.130231 restraints weight = 5221.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7120  Z= 0.243
  Angle     :  0.754   9.090   9570  Z= 0.398
  Chirality :  0.045   0.181   1060
  Planarity :  0.004   0.032   1240
  Dihedral  :  5.754  59.273   1005
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers : 11.51 %
    Allowed  : 27.95 %
    Favored  : 60.55 %
  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 (0.27), residues: 880
  helix:  0.38 (0.34), residues: 200
  sheet: -2.20 (0.28), residues: 300
  loop : -2.00 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  13 
 PHE   0.023   0.001   PHE F   8 
 TYR   0.011   0.001   TYR B  49 
 ARG   0.008   0.001   ARG G  62 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 236
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   41 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8022 (ttt90)
REVERT: J   68 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5716 (t80)
REVERT: A   41 ARG cc_start: 0.8420 (ttt90) cc_final: 0.8109 (ttt90)
REVERT: B   28 ARG cc_start: 0.8350 (mmm160) cc_final: 0.8074 (mmm-85)
REVERT: B   70 ARG cc_start: 0.5898 (ppt170) cc_final: 0.5341 (ppt170)
REVERT: C   73 LYS cc_start: 0.7716 (pttp) cc_final: 0.7383 (pttm)
REVERT: D   27 GLU cc_start: 0.8285 (tp30) cc_final: 0.7973 (tp30)
REVERT: D   28 ARG cc_start: 0.8463 (mmm160) cc_final: 0.7781 (mmm160)
REVERT: D   29 GLN cc_start: 0.7500 (pm20) cc_final: 0.6685 (pm20)
REVERT: D   49 TYR cc_start: 0.8691 (p90) cc_final: 0.8011 (p90)
REVERT: E   62 ARG cc_start: 0.8223 (ptp-110) cc_final: 0.7899 (ttm-80)
REVERT: E   68 PHE cc_start: 0.7809 (t80) cc_final: 0.7497 (t80)
REVERT: E   70 ARG cc_start: 0.5822 (ppt170) cc_final: 0.5379 (ppt170)
REVERT: F   73 LYS cc_start: 0.7907 (pttm) cc_final: 0.7458 (pttt)
REVERT: G   27 GLU cc_start: 0.8147 (tp30) cc_final: 0.7737 (tp30)
REVERT: G   34 ILE cc_start: 0.8401 (pt) cc_final: 0.8160 (pt)
REVERT: H   13 TRP cc_start: 0.8388 (p-90) cc_final: 0.8132 (p-90)
  outliers start: 84
  outliers final: 80
  residues processed: 282
  average time/residue: 0.2961
  time to fit residues: 101.3943
Evaluate side-chains
  311 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 230
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   11 ASN
Chi-restraints excluded: chain J residue   19 SER
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   34 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   57 THR
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   73 LYS
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   87 PHE
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   11 ASN
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   83 SER
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   11 ASN
Chi-restraints excluded: chain D residue   19 SER
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   36 CYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   41 ARG
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   87 PHE
Chi-restraints excluded: chain F residue   11 ASN
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   53 ILE
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain F residue   87 PHE
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   11 ASN
Chi-restraints excluded: chain G residue   21 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue   87 PHE
Chi-restraints excluded: chain H residue    1 ILE
Chi-restraints excluded: chain H residue   25 LEU
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   87 PHE
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   11 ASN
Chi-restraints excluded: chain I residue   21 VAL
Chi-restraints excluded: chain I residue   34 ILE
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   42 VAL
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   57 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0040
   chunk 0 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 60 optimal weight:    0.1980
   chunk 78 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.4992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.148392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.125750 restraints weight = 11892.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.129506 restraints weight = 7186.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.131958 restraints weight = 5078.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7120  Z= 0.224
  Angle     :  0.764   9.308   9570  Z= 0.402
  Chirality :  0.045   0.153   1060
  Planarity :  0.004   0.030   1240
  Dihedral  :  5.666  55.659   1005
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  9.86 %
    Allowed  : 30.14 %
    Favored  : 60.00 %
  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 (0.27), residues: 880
  helix:  0.51 (0.34), residues: 200
  sheet: -2.22 (0.28), residues: 300
  loop : -1.94 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  13 
 PHE   0.029   0.001   PHE F   8 
 TYR   0.013   0.001   TYR I  55 
 ARG   0.009   0.001   ARG I  62 

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 231
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   31 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8058 (mmtm)
REVERT: J   41 ARG cc_start: 0.8405 (ttt180) cc_final: 0.7999 (ttt90)
REVERT: J   68 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5596 (t80)
REVERT: A   28 ARG cc_start: 0.8652 (mmm160) cc_final: 0.8207 (mmm-85)
REVERT: A   41 ARG cc_start: 0.8385 (ttt90) cc_final: 0.8082 (ttt90)
REVERT: B   28 ARG cc_start: 0.8362 (mmm160) cc_final: 0.8103 (mmm-85)
REVERT: B   70 ARG cc_start: 0.5815 (ppt170) cc_final: 0.5280 (ppt170)
REVERT: C   73 LYS cc_start: 0.7644 (pttp) cc_final: 0.7205 (pttm)
REVERT: D   27 GLU cc_start: 0.8266 (tp30) cc_final: 0.7960 (tp30)
REVERT: D   28 ARG cc_start: 0.8441 (mmm160) cc_final: 0.7764 (mmm160)
REVERT: D   29 GLN cc_start: 0.7518 (pm20) cc_final: 0.6691 (pm20)
REVERT: D   49 TYR cc_start: 0.8646 (p90) cc_final: 0.8026 (p90)
REVERT: E   68 PHE cc_start: 0.7798 (t80) cc_final: 0.7464 (t80)
REVERT: E   70 ARG cc_start: 0.5701 (ppt170) cc_final: 0.5455 (ppt170)
REVERT: F   73 LYS cc_start: 0.7798 (pttm) cc_final: 0.7359 (pttt)
REVERT: G   27 GLU cc_start: 0.8202 (tp30) cc_final: 0.7769 (tp30)
REVERT: H   13 TRP cc_start: 0.8383 (p-90) cc_final: 0.8165 (p-90)
  outliers start: 72
  outliers final: 69
  residues processed: 268
  average time/residue: 0.2879
  time to fit residues: 92.8724
Evaluate side-chains
  293 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 223
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue    1 ILE
Chi-restraints excluded: chain J residue   11 ASN
Chi-restraints excluded: chain J residue   22 ILE
Chi-restraints excluded: chain J residue   34 ILE
Chi-restraints excluded: chain J residue   36 CYS
Chi-restraints excluded: chain J residue   40 VAL
Chi-restraints excluded: chain J residue   42 VAL
Chi-restraints excluded: chain J residue   57 THR
Chi-restraints excluded: chain J residue   68 PHE
Chi-restraints excluded: chain J residue   77 THR
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue   87 PHE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   36 CYS
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   73 LYS
Chi-restraints excluded: chain B residue    1 ILE
Chi-restraints excluded: chain B residue   22 ILE
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue   87 PHE
Chi-restraints excluded: chain C residue    1 ILE
Chi-restraints excluded: chain C residue   11 ASN
Chi-restraints excluded: chain C residue   34 ILE
Chi-restraints excluded: chain C residue   36 CYS
Chi-restraints excluded: chain C residue   42 VAL
Chi-restraints excluded: chain C residue   57 THR
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain D residue    1 ILE
Chi-restraints excluded: chain D residue   11 ASN
Chi-restraints excluded: chain D residue   19 SER
Chi-restraints excluded: chain D residue   34 ILE
Chi-restraints excluded: chain D residue   36 CYS
Chi-restraints excluded: chain D residue   37 THR
Chi-restraints excluded: chain D residue   41 ARG
Chi-restraints excluded: chain D residue   42 VAL
Chi-restraints excluded: chain D residue   57 THR
Chi-restraints excluded: chain E residue    1 ILE
Chi-restraints excluded: chain E residue   34 ILE
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain F residue   19 SER
Chi-restraints excluded: chain F residue   42 VAL
Chi-restraints excluded: chain F residue   53 ILE
Chi-restraints excluded: chain F residue   57 THR
Chi-restraints excluded: chain G residue    1 ILE
Chi-restraints excluded: chain G residue   21 VAL
Chi-restraints excluded: chain G residue   36 CYS
Chi-restraints excluded: chain G residue   42 VAL
Chi-restraints excluded: chain G residue   46 SER
Chi-restraints excluded: chain G residue   57 THR
Chi-restraints excluded: chain G residue   84 LEU
Chi-restraints excluded: chain G residue   87 PHE
Chi-restraints excluded: chain H residue    1 ILE
Chi-restraints excluded: chain H residue   34 ILE
Chi-restraints excluded: chain H residue   37 THR
Chi-restraints excluded: chain H residue   40 VAL
Chi-restraints excluded: chain H residue   42 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   87 PHE
Chi-restraints excluded: chain I residue    1 ILE
Chi-restraints excluded: chain I residue   34 ILE
Chi-restraints excluded: chain I residue   36 CYS
Chi-restraints excluded: chain I residue   40 VAL
Chi-restraints excluded: chain I residue   42 VAL
Chi-restraints excluded: chain I residue   53 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.6338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.148162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.125406 restraints weight = 11623.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.129136 restraints weight = 7000.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.131649 restraints weight = 4967.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7120  Z= 0.242
  Angle     :  0.796   9.149   9570  Z= 0.417
  Chirality :  0.046   0.168   1060
  Planarity :  0.004   0.082   1240
  Dihedral  :  5.681  55.566   1005
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers : 10.14 %
    Allowed  : 29.73 %
    Favored  : 60.14 %
  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: -2.31 (0.27), residues: 880
  helix:  0.51 (0.34), residues: 200
  sheet: -2.19 (0.28), residues: 300
  loop : -1.98 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  13 
 PHE   0.030   0.001   PHE F   8 
 TYR   0.013   0.001   TYR I  55 
 ARG   0.008   0.001   ARG G  62 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2747.02 seconds
wall clock time: 48 minutes 9.42 seconds (2889.42 seconds total)