Starting phenix.real_space_refine
on Wed Mar  4 06:51:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6se6_10152/03_2026/6se6_10152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6se6_10152/03_2026/6se6_10152.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/6se6_10152/03_2026/6se6_10152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6se6_10152/03_2026/6se6_10152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6se6_10152/03_2026/6se6_10152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6se6_10152/03_2026/6se6_10152.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      10      5.16       5
     C    6706      2.51       5
     N    2263      2.21       5
     O    2801      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12068
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 812
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "B"
      Number of atoms: 652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 652
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 776
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 812
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "F"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 672
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "V"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 160
          Classifications: {'peptide': 18}
          Link IDs: {'PTRANS': 1, 'TRANS': 16}
  Time building chain proxies: 2.54, per 1000 atoms: 0.21
  Number of scatterers: 12068
  At special positions: 0
  Unit cell: (78, 120.25, 114.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     288     15.00
     O    2801      8.00
     N    2263      7.00
     C    6706      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: 0.73
  Conformation dependent library (CDL) restraints added in 257.4 milliseconds
  

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 8 sheets defined
      69.4% alpha, 2.3% beta
      144 base pairs and 250 stacking pairs defined.
    Time for finding SS restraints: 1.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 57
      removed outlier: 4.271A  pdb=" N   LYS A  49 " --> pdb=" O   GLN A  45 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.526A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.808A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
      removed outlier: 3.547A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 3.705A  pdb=" N   ARG B  40 " --> pdb=" O   ARG B  36 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.234A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.668A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.673A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.458A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.599A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.836A  pdb=" N   ASN D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU D  71 " --> pdb=" O   ASN D  67 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 122
      removed outlier: 3.594A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR D 115 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 57
      removed outlier: 4.192A  pdb=" N   LYS E  49 " --> pdb=" O   GLN E  45 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.565A  pdb=" N   VAL E  76 " --> pdb=" O   ARG E  72 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 116
      removed outlier: 3.785A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LEU E 111 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU E 112 " --> pdb=" O   ASP E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 4.276A  pdb=" N   GLY E 134 " --> pdb=" O   ARG E 130 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 50 through 76
      removed outlier: 3.745A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE F  61 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.631A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 72
      removed outlier: 4.070A  pdb=" N   ASP G  72 " --> pdb=" O   ASN G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.654A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.990A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.771A  pdb=" N   ASN H  67 " --> pdb=" O   ASN H  63 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU H  71 " --> pdb=" O   ASN H  67 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ARG H  79 " --> pdb=" O   GLY H  75 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.511A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.594A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA H 110 " --> pdb=" O   LEU H 106 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR H 119 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 7.073A  pdb=" N   ASN A  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.658A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 120 through 121
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.678A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78

    351 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      359 hydrogen bonds
      686 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      250 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.32: 1874
        1.32 -     1.44: 4461
        1.44 -     1.56: 5947
        1.56 -     1.68: 580
        1.68 -     1.79: 18
  Bond restraints: 12880
  Sorted by residual:
  bond pdb=" CB  VAL C  27 "
       pdb=" CG2 VAL C  27 "
    ideal  model  delta    sigma   weight residual
    1.521  1.426  0.095 3.30e-02 9.18e+02 8.27e+00
  bond pdb=" C3'  DA J -38 "
       pdb=" O3'  DA J -38 "
    ideal  model  delta    sigma   weight residual
    1.422  1.482 -0.060 3.00e-02 1.11e+03 3.99e+00
  bond pdb=" CB  THR F  73 "
       pdb=" CG2 THR F  73 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.77e+00
  bond pdb=" CB  VAL G  27 "
       pdb=" CG2 VAL G  27 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.76e+00
  bond pdb=" C3'  DC I   4 "
       pdb=" O3'  DC I   4 "
    ideal  model  delta    sigma   weight residual
    1.422  1.480 -0.058 3.00e-02 1.11e+03 3.74e+00
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 18038
        2.43 -     4.87: 535
        4.87 -     7.30: 54
        7.30 -     9.74: 8
        9.74 -    12.17: 2
  Bond angle restraints: 18637
  Sorted by residual:
  angle pdb=" C   THR A  79 "
        pdb=" N   ARG A  80 "
        pdb=" CA  ARG A  80 "
      ideal   model   delta    sigma   weight residual
     121.54  128.72   -7.18 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" C   ARG A  44 "
        pdb=" N   GLN A  45 "
        pdb=" CA  GLN A  45 "
      ideal   model   delta    sigma   weight residual
     122.46  127.70   -5.24 1.41e+00 5.03e-01 1.38e+01
  angle pdb=" CA  TRP V 530 "
        pdb=" CB  TRP V 530 "
        pdb=" CG  TRP V 530 "
      ideal   model   delta    sigma   weight residual
     113.60  120.65   -7.05 1.90e+00 2.77e-01 1.38e+01
  angle pdb=" C3'  DA J -38 "
        pdb=" O3'  DA J -38 "
        pdb=" P    DG J -37 "
      ideal   model   delta    sigma   weight residual
     120.20  125.57   -5.37 1.50e+00 4.44e-01 1.28e+01
  angle pdb=" C3'  DC I -29 "
        pdb=" O3'  DC I -29 "
        pdb=" P    DT I -28 "
      ideal   model   delta    sigma   weight residual
     120.20  125.55   -5.35 1.50e+00 4.44e-01 1.27e+01
  ... (remaining 18632 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.73: 5551
       35.73 -    71.45: 1381
       71.45 -   107.18: 18
      107.18 -   142.90: 6
      142.90 -   178.63: 2
  Dihedral angle restraints: 6958
    sinusoidal: 4740
      harmonic: 2218
  Sorted by residual:
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.63 -178.63     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.72  144.28     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" C4'  DT J  54 "
           pdb=" C3'  DT J  54 "
           pdb=" O3'  DT J  54 "
           pdb=" P    DC J  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   94.35  125.65     1      3.50e+01 8.16e-04 1.24e+01
  ... (remaining 6955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1290
       0.047 -    0.093: 600
       0.093 -    0.140: 167
       0.140 -    0.187: 51
       0.187 -    0.233: 6
  Chirality restraints: 2114
  Sorted by residual:
  chirality pdb=" CG  LEU G  97 "
            pdb=" CB  LEU G  97 "
            pdb=" CD1 LEU G  97 "
            pdb=" CD2 LEU G  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  VAL B  21 "
            pdb=" N   VAL B  21 "
            pdb=" C   VAL B  21 "
            pdb=" CB  VAL B  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  VAL F  21 "
            pdb=" N   VAL F  21 "
            pdb=" C   VAL F  21 "
            pdb=" CB  VAL F  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 2111 not shown)

  Planarity restraints: 1347
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  26 "   -0.054 2.00e-02 2.50e+03   2.34e-02 1.64e+01
        pdb=" N9   DG I  26 "    0.056 2.00e-02 2.50e+03
        pdb=" C8   DG I  26 "    0.006 2.00e-02 2.50e+03
        pdb=" N7   DG I  26 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DG I  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DG I  26 "    0.001 2.00e-02 2.50e+03
        pdb=" O6   DG I  26 "   -0.019 2.00e-02 2.50e+03
        pdb=" N1   DG I  26 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2   DG I  26 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  26 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  26 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DG I  26 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  28 "   -0.043 2.00e-02 2.50e+03   1.98e-02 1.18e+01
        pdb=" N9   DG I  28 "    0.049 2.00e-02 2.50e+03
        pdb=" C8   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DG I  28 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DG I  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  28 "   -0.016 2.00e-02 2.50e+03
        pdb=" O6   DG I  28 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DG I  28 "    0.004 2.00e-02 2.50e+03
        pdb=" N2   DG I  28 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  28 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DG I  28 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I -26 "    0.044 2.00e-02 2.50e+03   2.06e-02 1.07e+01
        pdb=" N1   DT I -26 "   -0.043 2.00e-02 2.50e+03
        pdb=" C2   DT I -26 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DT I -26 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT I -26 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DT I -26 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT I -26 "    0.019 2.00e-02 2.50e+03
        pdb=" C5   DT I -26 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I -26 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DT I -26 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1344 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2460
        2.78 -     3.31: 10073
        3.31 -     3.84: 24303
        3.84 -     4.37: 27108
        4.37 -     4.90: 38480
  Nonbonded interactions: 102424
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  -4 "
            pdb=" N2   DG J   4 "
     model   vdw
     2.247 2.496
  nonbonded pdb=" O2   DC I -62 "
            pdb=" N2   DG J  62 "
     model   vdw
     2.249 2.496
  nonbonded pdb=" O2   DC I -56 "
            pdb=" N2   DG J  56 "
     model   vdw
     2.264 2.496
  nonbonded pdb=" N2   DG I -60 "
            pdb=" O2   DC J  60 "
     model   vdw
     2.268 2.496
  nonbonded pdb=" O2   DC I   5 "
            pdb=" N2   DG J  -5 "
     model   vdw
     2.275 2.496
  ... (remaining 102419 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 21 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 116)
}
ncs_group {
  reference = (chain 'D' and resid 35 through 124)
  selection = chain 'H'
}

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:             2.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.020
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
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      :  0.010   0.095  12880  Z= 0.448
  Angle     :  0.998  12.172  18637  Z= 0.571
  Chirality :  0.059   0.233   2114
  Planarity :  0.008   0.074   1347
  Dihedral  : 27.962 178.630   5528
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.83 (0.22), residues: 753
  helix: -2.55 (0.16), residues: 508
  sheet:  None (None), residues: 0
  loop : -2.06 (0.30), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 133 
 TYR   0.022   0.003   TYR G  50 
 PHE   0.016   0.003   PHE A  84 
 TRP   0.016   0.002   TRP V 530 
 HIS   0.015   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.01023 (12880)
  covalent geometry    : angle       0.99776 (18637)
  hydrogen bonds       : bond        0.14247 (  710)
  hydrogen bonds       : angle       4.96672 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.7960 (pp30) cc_final: 0.7738 (pm20)
REVERT: A   96 GLU cc_start: 0.8131 (tp30) cc_final: 0.7898 (mm-30)
REVERT: B   53 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8414 (tm-30)
REVERT: B   88 TYR cc_start: 0.8395 (m-10) cc_final: 0.8023 (m-10)
REVERT: C   56 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8308 (tm-30)
REVERT: C   75 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8644 (mmtm)
REVERT: D   59 MET cc_start: 0.8838 (tpp) cc_final: 0.8635 (tpp)
REVERT: D   63 ASN cc_start: 0.8898 (t0) cc_final: 0.8215 (t0)
REVERT: D   67 ASN cc_start: 0.8841 (m-40) cc_final: 0.8383 (t0)
REVERT: D   68 ASP cc_start: 0.8095 (t70) cc_final: 0.7869 (t0)
REVERT: D   71 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: D   76 GLU cc_start: 0.8063 (tp30) cc_final: 0.7842 (tp30)
REVERT: E   73 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: F   64 ASN cc_start: 0.8302 (t0) cc_final: 0.7761 (t0)
REVERT: F   88 TYR cc_start: 0.8906 (m-10) cc_final: 0.7888 (m-10)
REVERT: F   91 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8898 (ttpp)
REVERT: F   93 GLN cc_start: 0.7584 (mt0) cc_final: 0.6771 (mt0)
REVERT: G   64 GLU cc_start: 0.8568 (tp30) cc_final: 0.8344 (tp30)
REVERT: H   42 TYR cc_start: 0.7781 (t80) cc_final: 0.7298 (t80)
REVERT: H   68 ASP cc_start: 0.8689 (t0) cc_final: 0.8459 (t0)
REVERT: H   83 TYR cc_start: 0.8742 (m-10) cc_final: 0.8298 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1624
  time to fit residues: 49.3530
Evaluate side-chains
  180 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 127 GLN
B  27 GLN
B  93 GLN
C  31 HIS
C  73 ASN
H  67 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.085741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.059260 restraints weight = 39972.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.061182 restraints weight = 19266.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.062431 restraints weight = 12846.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.063165 restraints weight = 10282.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.063544 restraints weight = 9099.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12880  Z= 0.167
  Angle     :  0.609   6.120  18637  Z= 0.361
  Chirality :  0.034   0.181   2114
  Planarity :  0.004   0.045   1347
  Dihedral  : 30.755 175.732   4019
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.40 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.27), residues: 753
  helix: -0.01 (0.21), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.65 (0.33), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  29 
 TYR   0.016   0.002   TYR D  40 
 PHE   0.008   0.001   PHE A  84 
 TRP   0.010   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12880)
  covalent geometry    : angle       0.60852 (18637)
  hydrogen bonds       : bond        0.06532 (  710)
  hydrogen bonds       : angle       2.93988 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 223
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8204 (pp30) cc_final: 0.7808 (pm20)
REVERT: A  107 GLU cc_start: 0.8338 (pt0) cc_final: 0.8062 (pt0)
REVERT: A  127 GLN cc_start: 0.8279 (tp40) cc_final: 0.7994 (tp40)
REVERT: B   53 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: B   88 TYR cc_start: 0.8408 (m-10) cc_final: 0.8139 (m-10)
REVERT: B   91 LYS cc_start: 0.8860 (tttt) cc_final: 0.8222 (tptp)
REVERT: C   36 LYS cc_start: 0.9242 (mptt) cc_final: 0.8990 (mmtm)
REVERT: C   56 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8534 (tm-30)
REVERT: C   57 TYR cc_start: 0.9157 (t80) cc_final: 0.8844 (t80)
REVERT: C   61 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8271 (tm-30)
REVERT: C   71 ARG cc_start: 0.8908 (ttm110) cc_final: 0.8497 (ttp80)
REVERT: D   34 LYS cc_start: 0.9142 (mmmm) cc_final: 0.8246 (mptt)
REVERT: D   35 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6237 (mm-30)
REVERT: D   67 ASN cc_start: 0.8775 (m-40) cc_final: 0.8169 (t0)
REVERT: D   68 ASP cc_start: 0.8512 (t70) cc_final: 0.8208 (t0)
REVERT: D   71 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8118 (tm-30)
REVERT: E   73 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: E  132 ILE cc_start: 0.8616 (tt) cc_final: 0.8401 (tt)
REVERT: F   64 ASN cc_start: 0.9063 (t0) cc_final: 0.8239 (t0)
REVERT: F   91 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8709 (ttpp)
REVERT: F   93 GLN cc_start: 0.7745 (mt0) cc_final: 0.6752 (mt0)
REVERT: G   64 GLU cc_start: 0.8908 (tp30) cc_final: 0.8293 (tp30)
REVERT: G   92 GLU cc_start: 0.6949 (tt0) cc_final: 0.6431 (tt0)
REVERT: H   42 TYR cc_start: 0.7888 (t80) cc_final: 0.7429 (t80)
REVERT: H   68 ASP cc_start: 0.9252 (t0) cc_final: 0.8754 (t0)
REVERT: H   83 TYR cc_start: 0.8753 (m-10) cc_final: 0.8198 (m-80)
REVERT: H   93 GLU cc_start: 0.8854 (mp0) cc_final: 0.8654 (mp0)
  outliers start: 8
  outliers final: 6
  residues processed: 225
  average time/residue: 0.1305
  time to fit residues: 39.6066
Evaluate side-chains
  195 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 189
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 80 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 82 optimal weight:   10.0000
   chunk 35 optimal weight:    4.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
H  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.084944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.057667 restraints weight = 40897.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.059466 restraints weight = 20490.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.060627 restraints weight = 14008.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.061336 restraints weight = 11346.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.061718 restraints weight = 10146.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12880  Z= 0.237
  Angle     :  0.627   7.133  18637  Z= 0.367
  Chirality :  0.036   0.166   2114
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.659 173.642   4019
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.59 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.29), residues: 753
  helix:  1.06 (0.23), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.60 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  39 
 TYR   0.022   0.002   TYR D  83 
 PHE   0.008   0.001   PHE E 101 
 TRP   0.008   0.001   TRP V 530 
 HIS   0.009   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (12880)
  covalent geometry    : angle       0.62661 (18637)
  hydrogen bonds       : bond        0.06453 (  710)
  hydrogen bonds       : angle       2.93561 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8223 (pp30) cc_final: 0.7848 (pm20)
REVERT: A  107 GLU cc_start: 0.8307 (pt0) cc_final: 0.7988 (pt0)
REVERT: A  127 GLN cc_start: 0.8576 (tp40) cc_final: 0.8225 (tp40)
REVERT: B   53 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8303 (tm-30)
REVERT: B   91 LYS cc_start: 0.8845 (tttt) cc_final: 0.8283 (tptp)
REVERT: C   36 LYS cc_start: 0.9230 (mptt) cc_final: 0.9006 (mmtm)
REVERT: C   56 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8777 (tm-30)
REVERT: C   71 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8584 (ttp80)
REVERT: D   34 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8325 (mptt)
REVERT: D   67 ASN cc_start: 0.8732 (m-40) cc_final: 0.8181 (t0)
REVERT: D   68 ASP cc_start: 0.8606 (t70) cc_final: 0.8317 (t0)
REVERT: D   71 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: E   73 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: F   24 ASP cc_start: 0.8766 (t0) cc_final: 0.8493 (t0)
REVERT: F   64 ASN cc_start: 0.9115 (t0) cc_final: 0.8336 (t0)
REVERT: F   91 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8688 (ttpp)
REVERT: F   93 GLN cc_start: 0.7919 (mt0) cc_final: 0.6942 (mt0)
REVERT: G   24 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8024 (mp10)
REVERT: G   92 GLU cc_start: 0.6531 (tt0) cc_final: 0.5863 (tt0)
REVERT: H   42 TYR cc_start: 0.7878 (t80) cc_final: 0.7580 (t80)
REVERT: H   67 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8807 (t0)
REVERT: H   68 ASP cc_start: 0.9318 (t0) cc_final: 0.8848 (t0)
REVERT: H   83 TYR cc_start: 0.8733 (m-10) cc_final: 0.8381 (m-80)
  outliers start: 20
  outliers final: 15
  residues processed: 199
  average time/residue: 0.1170
  time to fit residues: 32.0974
Evaluate side-chains
  197 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain H residue   67 ASN
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0870
   chunk 66 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 90 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.7764

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
F  75 HIS
H  67 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.086225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.059227 restraints weight = 40470.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.061105 restraints weight = 20238.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.062306 restraints weight = 13762.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.063013 restraints weight = 11111.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.063377 restraints weight = 9902.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12880  Z= 0.176
  Angle     :  0.584   5.583  18637  Z= 0.346
  Chirality :  0.034   0.162   2114
  Planarity :  0.004   0.042   1347
  Dihedral  : 30.594 173.142   4019
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 22.10 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.30), residues: 753
  helix:  1.48 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.40 (0.35), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  35 
 TYR   0.026   0.002   TYR D  83 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.005   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12880)
  covalent geometry    : angle       0.58365 (18637)
  hydrogen bonds       : bond        0.05969 (  710)
  hydrogen bonds       : angle       2.67634 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 200
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8261 (pp30) cc_final: 0.7893 (pm20)
REVERT: A  104 HIS cc_start: 0.7728 (m90) cc_final: 0.7416 (t70)
REVERT: A  127 GLN cc_start: 0.8519 (tp40) cc_final: 0.8108 (tp40)
REVERT: B   53 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8681 (tm-30)
REVERT: B   91 LYS cc_start: 0.8809 (tttt) cc_final: 0.8264 (tptp)
REVERT: C   36 LYS cc_start: 0.9240 (mptt) cc_final: 0.9013 (mmtm)
REVERT: C   56 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8490 (tm-30)
REVERT: C   57 TYR cc_start: 0.9148 (t80) cc_final: 0.8846 (t80)
REVERT: C   71 ARG cc_start: 0.8967 (ttm110) cc_final: 0.8619 (ttp80)
REVERT: D   34 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8383 (mptt)
REVERT: D   67 ASN cc_start: 0.8694 (m-40) cc_final: 0.8131 (t0)
REVERT: D   68 ASP cc_start: 0.8489 (t70) cc_final: 0.8214 (t0)
REVERT: D   71 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: E   73 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: F   24 ASP cc_start: 0.8746 (t0) cc_final: 0.8470 (t0)
REVERT: F   27 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8023 (tm-30)
REVERT: F   64 ASN cc_start: 0.9136 (t0) cc_final: 0.8519 (t0)
REVERT: F   88 TYR cc_start: 0.8663 (m-10) cc_final: 0.7920 (m-10)
REVERT: F   91 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8663 (ttpp)
REVERT: G   24 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8140 (mp10)
REVERT: G   81 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7794 (tpt170)
REVERT: H   42 TYR cc_start: 0.7806 (t80) cc_final: 0.7559 (t80)
REVERT: H   68 ASP cc_start: 0.9284 (t0) cc_final: 0.8860 (t0)
REVERT: H   83 TYR cc_start: 0.8669 (m-10) cc_final: 0.8428 (m-80)
REVERT: H   93 GLU cc_start: 0.8762 (mp0) cc_final: 0.8417 (mp0)
  outliers start: 25
  outliers final: 14
  residues processed: 209
  average time/residue: 0.1226
  time to fit residues: 35.1782
Evaluate side-chains
  202 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   79 THR
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   46 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:   20.0000
   chunk 90 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 47 optimal weight:    8.9990
   chunk 78 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
D  82 HIS
H  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.084333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.056851 restraints weight = 40311.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.058649 restraints weight = 20399.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.059792 restraints weight = 13993.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.060433 restraints weight = 11358.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.060799 restraints weight = 10181.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12880  Z= 0.268
  Angle     :  0.640   7.504  18637  Z= 0.372
  Chirality :  0.037   0.162   2114
  Planarity :  0.004   0.041   1347
  Dihedral  : 30.742 169.383   4019
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 23.20 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.30), residues: 753
  helix:  1.53 (0.23), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.34 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  39 
 TYR   0.046   0.002   TYR D  83 
 PHE   0.011   0.001   PHE E  84 
 TRP   0.005   0.001   TRP V 530 
 HIS   0.011   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (12880)
  covalent geometry    : angle       0.64031 (18637)
  hydrogen bonds       : bond        0.06442 (  710)
  hydrogen bonds       : angle       3.04214 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8241 (pp30) cc_final: 0.7863 (pm20)
REVERT: A  107 GLU cc_start: 0.8290 (pt0) cc_final: 0.7939 (pt0)
REVERT: A  127 GLN cc_start: 0.8620 (tp40) cc_final: 0.8233 (tp40)
REVERT: B   53 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8757 (tm-30)
REVERT: B   91 LYS cc_start: 0.8860 (tttt) cc_final: 0.8300 (tptp)
REVERT: C   36 LYS cc_start: 0.9217 (mptt) cc_final: 0.8961 (mmtm)
REVERT: C   56 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8767 (tm-30)
REVERT: C   71 ARG cc_start: 0.9040 (ttm110) cc_final: 0.8694 (ttp80)
REVERT: D   34 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8350 (mptt)
REVERT: D   68 ASP cc_start: 0.8596 (t70) cc_final: 0.8193 (t0)
REVERT: D   71 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: E   53 LYS cc_start: 0.9295 (tppp) cc_final: 0.8967 (tppt)
REVERT: E   73 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: F   24 ASP cc_start: 0.8709 (t0) cc_final: 0.8460 (t0)
REVERT: F   64 ASN cc_start: 0.9141 (t0) cc_final: 0.8264 (t0)
REVERT: F   88 TYR cc_start: 0.8709 (m-10) cc_final: 0.7884 (m-10)
REVERT: F   91 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8759 (ttpp)
REVERT: F   93 GLN cc_start: 0.8036 (mt0) cc_final: 0.6967 (mt0)
REVERT: G   24 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8100 (mp10)
REVERT: G   90 ASP cc_start: 0.7215 (t0) cc_final: 0.6843 (t0)
REVERT: G   92 GLU cc_start: 0.6334 (tt0) cc_final: 0.5885 (tt0)
REVERT: G  111 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6543 (pt)
REVERT: H   42 TYR cc_start: 0.7884 (t80) cc_final: 0.7679 (t80)
REVERT: H   68 ASP cc_start: 0.9345 (t0) cc_final: 0.8878 (t0)
REVERT: H   83 TYR cc_start: 0.8769 (m-10) cc_final: 0.8342 (m-80)
REVERT: H   93 GLU cc_start: 0.8817 (mp0) cc_final: 0.8490 (mp0)
  outliers start: 32
  outliers final: 25
  residues processed: 200
  average time/residue: 0.1124
  time to fit residues: 31.3317
Evaluate side-chains
  203 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 88 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.085924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.058880 restraints weight = 40658.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.060727 restraints weight = 20425.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.061907 restraints weight = 13938.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.062603 restraints weight = 11288.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.062947 restraints weight = 10071.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12880  Z= 0.171
  Angle     :  0.584   7.530  18637  Z= 0.344
  Chirality :  0.033   0.159   2114
  Planarity :  0.003   0.043   1347
  Dihedral  : 30.625 168.492   4019
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 27.12 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.30), residues: 753
  helix:  1.65 (0.23), residues: 517
  sheet:  None (None), residues: 0
  loop : -1.19 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  35 
 TYR   0.045   0.002   TYR D  83 
 PHE   0.009   0.001   PHE A  78 
 TRP   0.005   0.001   TRP E  47 
 HIS   0.023   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12880)
  covalent geometry    : angle       0.58447 (18637)
  hydrogen bonds       : bond        0.05904 (  710)
  hydrogen bonds       : angle       2.69402 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 190
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8262 (pp30) cc_final: 0.7893 (pm20)
REVERT: A  107 GLU cc_start: 0.8312 (pt0) cc_final: 0.7962 (pt0)
REVERT: A  127 GLN cc_start: 0.8563 (tp40) cc_final: 0.8136 (tp40)
REVERT: B   53 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8632 (tm-30)
REVERT: B   91 LYS cc_start: 0.8826 (tttt) cc_final: 0.8294 (tptp)
REVERT: C   36 LYS cc_start: 0.9214 (mptt) cc_final: 0.8955 (mmtm)
REVERT: C   56 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8706 (tm-30)
REVERT: C   57 TYR cc_start: 0.9142 (t80) cc_final: 0.8895 (t80)
REVERT: C   71 ARG cc_start: 0.9067 (ttm110) cc_final: 0.8718 (ttp80)
REVERT: D   34 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8380 (mptt)
REVERT: D   67 ASN cc_start: 0.8651 (m-40) cc_final: 0.8109 (t0)
REVERT: D   68 ASP cc_start: 0.8485 (t70) cc_final: 0.8237 (t0)
REVERT: D   71 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: E   43 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.8005 (ptt-90)
REVERT: E   53 LYS cc_start: 0.9271 (tppp) cc_final: 0.8943 (tppt)
REVERT: E   73 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8181 (tm-30)
REVERT: F   24 ASP cc_start: 0.8710 (t0) cc_final: 0.8462 (t0)
REVERT: F   64 ASN cc_start: 0.9165 (t0) cc_final: 0.8260 (t0)
REVERT: F   88 TYR cc_start: 0.8680 (m-10) cc_final: 0.7828 (m-10)
REVERT: F   91 LYS cc_start: 0.8937 (ttmt) cc_final: 0.8696 (ttpp)
REVERT: F   93 GLN cc_start: 0.8010 (mt0) cc_final: 0.7021 (mt0)
REVERT: G   24 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7988 (mp10)
REVERT: G   92 GLU cc_start: 0.6257 (tt0) cc_final: 0.5716 (tt0)
REVERT: G  111 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6587 (pt)
REVERT: H   68 ASP cc_start: 0.9251 (t0) cc_final: 0.8792 (t0)
REVERT: H   76 GLU cc_start: 0.8477 (tp30) cc_final: 0.8208 (tp30)
REVERT: H   83 TYR cc_start: 0.8674 (m-10) cc_final: 0.8323 (m-80)
REVERT: H   93 GLU cc_start: 0.8819 (mp0) cc_final: 0.8452 (mp0)
  outliers start: 18
  outliers final: 15
  residues processed: 198
  average time/residue: 0.1137
  time to fit residues: 31.4240
Evaluate side-chains
  200 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   43 ARG
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.085778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.058602 restraints weight = 40608.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.060474 restraints weight = 20531.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.061645 restraints weight = 14047.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.062335 restraints weight = 11376.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.062729 restraints weight = 10165.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12880  Z= 0.184
  Angle     :  0.594   7.535  18637  Z= 0.348
  Chirality :  0.034   0.160   2114
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.582 166.722   4019
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 28.21 %
    Favored  : 68.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.30), residues: 753
  helix:  1.68 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.14 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG V 522 
 TYR   0.069   0.002   TYR D  83 
 PHE   0.014   0.001   PHE A  67 
 TRP   0.004   0.001   TRP E  47 
 HIS   0.004   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (12880)
  covalent geometry    : angle       0.59360 (18637)
  hydrogen bonds       : bond        0.05926 (  710)
  hydrogen bonds       : angle       2.70481 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 184
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8254 (pp30) cc_final: 0.7876 (pm20)
REVERT: A   96 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8396 (mm-30)
REVERT: A  107 GLU cc_start: 0.8281 (pt0) cc_final: 0.7932 (pt0)
REVERT: A  127 GLN cc_start: 0.8558 (tp40) cc_final: 0.8120 (tp40)
REVERT: B   53 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: B   91 LYS cc_start: 0.8797 (tttt) cc_final: 0.8287 (tptp)
REVERT: B   93 GLN cc_start: 0.8232 (tt0) cc_final: 0.8029 (tt0)
REVERT: C   36 LYS cc_start: 0.9203 (mptt) cc_final: 0.8939 (mmtm)
REVERT: C   56 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8724 (tm-30)
REVERT: C   57 TYR cc_start: 0.9124 (t80) cc_final: 0.8861 (t80)
REVERT: C   71 ARG cc_start: 0.9083 (ttm110) cc_final: 0.8719 (ttp80)
REVERT: D   34 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8357 (mptt)
REVERT: D   68 ASP cc_start: 0.8502 (t70) cc_final: 0.8104 (t0)
REVERT: D   71 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8239 (tm-30)
REVERT: E   43 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8024 (ptt-90)
REVERT: E   53 LYS cc_start: 0.9282 (tppp) cc_final: 0.8950 (tppt)
REVERT: E   73 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: F   24 ASP cc_start: 0.8721 (t0) cc_final: 0.8476 (t0)
REVERT: F   64 ASN cc_start: 0.9181 (t0) cc_final: 0.8275 (t0)
REVERT: F   88 TYR cc_start: 0.8632 (m-10) cc_final: 0.7778 (m-10)
REVERT: F   91 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8674 (ttpp)
REVERT: F   93 GLN cc_start: 0.8017 (mt0) cc_final: 0.7021 (mt0)
REVERT: G   24 GLN cc_start: 0.8595 (mm-40) cc_final: 0.7974 (mp10)
REVERT: G  111 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6584 (pt)
REVERT: H   68 ASP cc_start: 0.9281 (t0) cc_final: 0.8786 (t0)
REVERT: H   76 GLU cc_start: 0.8495 (tp30) cc_final: 0.8199 (tp30)
REVERT: H   83 TYR cc_start: 0.8689 (m-10) cc_final: 0.8326 (m-80)
REVERT: H   93 GLU cc_start: 0.8844 (mp0) cc_final: 0.8532 (mp0)
  outliers start: 22
  outliers final: 17
  residues processed: 194
  average time/residue: 0.1164
  time to fit residues: 31.4128
Evaluate side-chains
  197 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 178
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   43 ARG
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
D  82 HIS
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.086832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.059896 restraints weight = 40683.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.061759 restraints weight = 20555.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.062964 restraints weight = 14009.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.063652 restraints weight = 11310.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.064050 restraints weight = 10094.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12880  Z= 0.167
  Angle     :  0.588   7.562  18637  Z= 0.346
  Chirality :  0.033   0.174   2114
  Planarity :  0.003   0.044   1347
  Dihedral  : 30.466 163.085   4019
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 29.00 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.30), residues: 753
  helix:  1.81 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.19 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG V 522 
 TYR   0.055   0.002   TYR D  83 
 PHE   0.017   0.001   PHE A  84 
 TRP   0.005   0.001   TRP E  47 
 HIS   0.014   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (12880)
  covalent geometry    : angle       0.58843 (18637)
  hydrogen bonds       : bond        0.05852 (  710)
  hydrogen bonds       : angle       2.62389 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8243 (pp30) cc_final: 0.7904 (pm20)
REVERT: A   96 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8392 (tp30)
REVERT: A  127 GLN cc_start: 0.8524 (tp40) cc_final: 0.8069 (tp40)
REVERT: B   53 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8554 (tm-30)
REVERT: B   91 LYS cc_start: 0.8781 (tttt) cc_final: 0.8158 (tptp)
REVERT: B   93 GLN cc_start: 0.8254 (tt0) cc_final: 0.8049 (tt0)
REVERT: C   36 LYS cc_start: 0.9215 (mptt) cc_final: 0.8939 (mmtm)
REVERT: C   39 TYR cc_start: 0.8963 (m-80) cc_final: 0.8717 (m-80)
REVERT: C   56 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8493 (tm-30)
REVERT: C   57 TYR cc_start: 0.9109 (t80) cc_final: 0.8811 (t80)
REVERT: C   71 ARG cc_start: 0.9070 (ttm110) cc_final: 0.8713 (ttp80)
REVERT: C   81 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7644 (tpt170)
REVERT: D   34 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8368 (mptt)
REVERT: D   68 ASP cc_start: 0.8441 (t70) cc_final: 0.8052 (t0)
REVERT: D   71 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: E   43 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8010 (ptt-90)
REVERT: E   53 LYS cc_start: 0.9273 (tppp) cc_final: 0.8960 (tppt)
REVERT: E   73 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: F   24 ASP cc_start: 0.8697 (t0) cc_final: 0.8451 (t0)
REVERT: F   64 ASN cc_start: 0.9195 (t0) cc_final: 0.8286 (t0)
REVERT: F   88 TYR cc_start: 0.8607 (m-10) cc_final: 0.7779 (m-10)
REVERT: F   91 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8688 (ttpp)
REVERT: F   93 GLN cc_start: 0.8042 (mt0) cc_final: 0.7073 (mt0)
REVERT: G   24 GLN cc_start: 0.8578 (mm-40) cc_final: 0.7975 (mp10)
REVERT: G  111 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6614 (pt)
REVERT: H   68 ASP cc_start: 0.9226 (t0) cc_final: 0.8755 (t0)
REVERT: H   76 GLU cc_start: 0.8487 (tp30) cc_final: 0.8161 (tp30)
REVERT: H   83 TYR cc_start: 0.8643 (m-10) cc_final: 0.8317 (m-80)
REVERT: H   93 GLU cc_start: 0.8823 (mp0) cc_final: 0.8560 (mp0)
REVERT: V  522 ARG cc_start: 0.3625 (ptm160) cc_final: 0.3061 (ptm160)
  outliers start: 22
  outliers final: 18
  residues processed: 201
  average time/residue: 0.1138
  time to fit residues: 32.0863
Evaluate side-chains
  205 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain E residue   43 ARG
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  523 ILE
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.085636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.059311 restraints weight = 40974.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.061174 restraints weight = 20183.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.062383 restraints weight = 13585.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.063074 restraints weight = 10858.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.063447 restraints weight = 9630.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12880  Z= 0.184
  Angle     :  0.599   7.809  18637  Z= 0.352
  Chirality :  0.034   0.169   2114
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.454 159.714   4019
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 29.00 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.30), residues: 753
  helix:  1.78 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.19 (0.36), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.087   0.003   TYR D  83 
 PHE   0.019   0.001   PHE A  84 
 TRP   0.004   0.001   TRP E  47 
 HIS   0.018   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (12880)
  covalent geometry    : angle       0.59949 (18637)
  hydrogen bonds       : bond        0.05919 (  710)
  hydrogen bonds       : angle       2.66472 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 181
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8213 (pp30) cc_final: 0.7893 (pm20)
REVERT: A  127 GLN cc_start: 0.8551 (tp40) cc_final: 0.8112 (tp40)
REVERT: B   53 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8551 (tm-30)
REVERT: B   91 LYS cc_start: 0.8790 (tttt) cc_final: 0.8232 (tptp)
REVERT: B   93 GLN cc_start: 0.8257 (tt0) cc_final: 0.7995 (tt0)
REVERT: C   36 LYS cc_start: 0.9231 (mptt) cc_final: 0.8944 (mmtm)
REVERT: C   39 TYR cc_start: 0.8914 (m-80) cc_final: 0.8693 (m-80)
REVERT: C   56 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8507 (tm-30)
REVERT: C   57 TYR cc_start: 0.9145 (t80) cc_final: 0.8844 (t80)
REVERT: C   71 ARG cc_start: 0.9061 (ttm110) cc_final: 0.8718 (ttp80)
REVERT: D   34 LYS cc_start: 0.9209 (mmmm) cc_final: 0.8392 (mptt)
REVERT: D   62 MET cc_start: 0.8534 (mmm) cc_final: 0.7720 (mmm)
REVERT: D   68 ASP cc_start: 0.8491 (t70) cc_final: 0.8103 (t0)
REVERT: D   71 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8299 (tm-30)
REVERT: E   43 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8035 (ptt-90)
REVERT: E   53 LYS cc_start: 0.9289 (tppp) cc_final: 0.8992 (tppt)
REVERT: E   73 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: F   24 ASP cc_start: 0.8684 (t0) cc_final: 0.8450 (t0)
REVERT: F   64 ASN cc_start: 0.9153 (t0) cc_final: 0.8232 (t0)
REVERT: F   88 TYR cc_start: 0.8667 (m-10) cc_final: 0.7749 (m-10)
REVERT: F   91 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8790 (ttpp)
REVERT: F   93 GLN cc_start: 0.8083 (mt0) cc_final: 0.7086 (mt0)
REVERT: G   24 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8008 (mp10)
REVERT: G  111 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6666 (pt)
REVERT: H   68 ASP cc_start: 0.9217 (t0) cc_final: 0.8749 (t0)
REVERT: H   76 GLU cc_start: 0.8497 (tp30) cc_final: 0.8180 (tp30)
REVERT: H   83 TYR cc_start: 0.8666 (m-10) cc_final: 0.8322 (m-80)
REVERT: H   93 GLU cc_start: 0.8821 (mp0) cc_final: 0.8599 (mp0)
  outliers start: 22
  outliers final: 18
  residues processed: 190
  average time/residue: 0.1074
  time to fit residues: 28.9999
Evaluate side-chains
  200 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   43 ARG
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  523 ILE
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 72 optimal weight:   20.0000
   chunk 30 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 80 optimal weight:   10.0000
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.086993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.060697 restraints weight = 40987.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.062632 restraints weight = 20299.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.063866 restraints weight = 13601.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.064588 restraints weight = 10820.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.064963 restraints weight = 9574.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12880  Z= 0.163
  Angle     :  0.599   8.495  18637  Z= 0.349
  Chirality :  0.033   0.240   2114
  Planarity :  0.003   0.045   1347
  Dihedral  : 30.375 161.830   4019
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 30.25 %
    Favored  : 66.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.30), residues: 753
  helix:  1.96 (0.23), residues: 511
  sheet:  None (None), residues: 0
  loop : -1.09 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  86 
 TYR   0.034   0.002   TYR D  83 
 PHE   0.016   0.001   PHE A  84 
 TRP   0.005   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (12880)
  covalent geometry    : angle       0.59950 (18637)
  hydrogen bonds       : bond        0.05826 (  710)
  hydrogen bonds       : angle       2.62444 ( 1730)

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

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

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1506 Ramachandran restraints generated.
    753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 184
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8199 (pp30) cc_final: 0.7912 (pm20)
REVERT: A  127 GLN cc_start: 0.8511 (tp40) cc_final: 0.8052 (tp40)
REVERT: B   53 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: B   84 MET cc_start: 0.8389 (tpp) cc_final: 0.8025 (tpp)
REVERT: B   91 LYS cc_start: 0.8590 (tttt) cc_final: 0.8132 (tptp)
REVERT: B   93 GLN cc_start: 0.8132 (tt0) cc_final: 0.7875 (tt0)
REVERT: C   36 LYS cc_start: 0.9212 (mptt) cc_final: 0.8920 (mmtm)
REVERT: C   56 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8498 (tm-30)
REVERT: C   57 TYR cc_start: 0.9061 (t80) cc_final: 0.8772 (t80)
REVERT: C   71 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8717 (ttp80)
REVERT: C   81 ARG cc_start: 0.8077 (tpt170) cc_final: 0.7801 (tpt170)
REVERT: D   34 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8393 (mptt)
REVERT: D   47 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8811 (tt0)
REVERT: D   68 ASP cc_start: 0.8434 (t70) cc_final: 0.8077 (t0)
REVERT: D   71 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: E   43 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8030 (ptt-90)
REVERT: E   45 GLN cc_start: 0.8525 (pt0) cc_final: 0.8055 (pp30)
REVERT: E   53 LYS cc_start: 0.9278 (tppp) cc_final: 0.8980 (tppt)
REVERT: F   24 ASP cc_start: 0.8695 (t0) cc_final: 0.8476 (t0)
REVERT: F   64 ASN cc_start: 0.9206 (t0) cc_final: 0.8279 (t0)
REVERT: F   88 TYR cc_start: 0.8609 (m-10) cc_final: 0.7809 (m-10)
REVERT: F   91 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8773 (ttpp)
REVERT: F   93 GLN cc_start: 0.8057 (mt0) cc_final: 0.7126 (mt0)
REVERT: G   24 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8028 (mp10)
REVERT: G  111 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6627 (pt)
REVERT: H   68 ASP cc_start: 0.9214 (t0) cc_final: 0.8775 (t0)
REVERT: H   76 GLU cc_start: 0.8473 (tp30) cc_final: 0.8137 (tp30)
REVERT: H   83 TYR cc_start: 0.8614 (m-10) cc_final: 0.8344 (m-80)
REVERT: H   93 GLU cc_start: 0.8821 (mp0) cc_final: 0.8601 (mp0)
  outliers start: 22
  outliers final: 17
  residues processed: 195
  average time/residue: 0.1167
  time to fit residues: 31.9273
Evaluate side-chains
  199 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   43 ARG
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   79 ARG
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain V residue  523 ILE
Chi-restraints excluded: chain V residue  532 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 54 optimal weight:    0.3980
   chunk 77 optimal weight:   10.0000
   chunk 11 optimal weight:    8.9990
   chunk 99 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.085946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.059311 restraints weight = 40786.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.061141 restraints weight = 20532.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.062336 restraints weight = 13946.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.063038 restraints weight = 11221.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.063435 restraints weight = 9943.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12880  Z= 0.188
  Angle     :  0.603   8.054  18637  Z= 0.350
  Chirality :  0.034   0.179   2114
  Planarity :  0.003   0.044   1347
  Dihedral  : 30.427 164.298   4019
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 30.56 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.30), residues: 753
  helix:  1.95 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.14 (0.35), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  29 
 TYR   0.037   0.002   TYR D  83 
 PHE   0.014   0.001   PHE A  84 
 TRP   0.004   0.001   TRP E  47 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (12880)
  covalent geometry    : angle       0.60335 (18637)
  hydrogen bonds       : bond        0.05828 (  710)
  hydrogen bonds       : angle       2.68216 ( 1730)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1905.88 seconds
wall clock time: 33 minutes 37.29 seconds (2017.29 seconds total)