Starting phenix.real_space_refine
on Fri Sep 11 21:09:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6se6_10152/09_2026/6se6_10152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6se6_10152/09_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_10152/09_2026/6se6_10152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6se6_10152/09_2026/6se6_10152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6se6_10152/09_2026/6se6_10152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6se6_10152/09_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-2.2.1-6174/lib/python3.11/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: 2.56, 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: 1.02
  Conformation dependent library (CDL) restraints added in 385.1 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: 1.71
  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: 2.18

  Time building geometry restraints manager: 1.39 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=" C3'  DC J -58 "
       pdb=" C2'  DC J -58 "
    ideal  model  delta    sigma   weight residual
    1.516  1.551 -0.035 8.00e-03 1.56e+04 1.93e+01
  bond pdb=" C3'  DT I  15 "
       pdb=" C2'  DT I  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 8.00e-03 1.56e+04 1.68e+01
  bond pdb=" C3'  DT J -17 "
       pdb=" C2'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.55e+01
  bond pdb=" N7   DA I  17 "
       pdb=" C5   DA I  17 "
    ideal  model  delta    sigma   weight residual
    1.388  1.365  0.023 6.00e-03 2.78e+04 1.50e+01
  bond pdb=" N1   DC I   8 "
       pdb=" C6   DC I   8 "
    ideal  model  delta    sigma   weight residual
    1.367  1.344  0.023 6.00e-03 2.78e+04 1.45e+01
  ... (remaining 12875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 17781
        2.43 -     4.87: 776
        4.87 -     7.30: 70
        7.30 -     9.74: 8
        9.74 -    12.17: 2
  Bond angle restraints: 18637
  Sorted by residual:
  angle pdb=" O4'  DG I  26 "
        pdb=" C1'  DG I  26 "
        pdb=" N9   DG I  26 "
      ideal   model   delta    sigma   weight residual
     108.00  103.35    4.65 7.00e-01 2.04e+00 4.42e+01
  angle pdb=" O4'  DA J  16 "
        pdb=" C1'  DA J  16 "
        pdb=" N9   DA J  16 "
      ideal   model   delta    sigma   weight residual
     108.00  111.95   -3.95 7.00e-01 2.04e+00 3.19e+01
  angle pdb=" O4'  DG I  28 "
        pdb=" C1'  DG I  28 "
        pdb=" N9   DG I  28 "
      ideal   model   delta    sigma   weight residual
     108.00  104.14    3.86 7.00e-01 2.04e+00 3.04e+01
  angle pdb=" O4'  DT J -32 "
        pdb=" C1'  DT J -32 "
        pdb=" N1   DT J -32 "
      ideal   model   delta    sigma   weight residual
     108.00  111.81   -3.81 7.00e-01 2.04e+00 2.96e+01
  angle pdb=" O4'  DT J -61 "
        pdb=" C4'  DT J -61 "
        pdb=" C3'  DT J -61 "
      ideal   model   delta    sigma   weight residual
     106.00  102.94    3.06 6.00e-01 2.78e+00 2.60e+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 -    0.048: 1165
       0.048 -    0.095: 638
       0.095 -    0.143: 245
       0.143 -    0.191: 57
       0.191 -    0.238: 9
  Chirality restraints: 2114
  Sorted by residual:
  chirality pdb=" C3'  DG J  20 "
            pdb=" C4'  DG J  20 "
            pdb=" O3'  DG J  20 "
            pdb=" C2'  DG J  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.49   -0.24 2.00e-01 2.50e+01 1.42e+00
  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=" C3'  DT J  54 "
            pdb=" C4'  DT J  54 "
            pdb=" O3'  DT J  54 "
            pdb=" C2'  DT J  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.50   -0.23 2.00e-01 2.50e+01 1.32e+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:             3.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.040
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
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      :  0.011   0.095  12880  Z= 0.833
  Angle     :  1.111  12.172  18637  Z= 0.859
  Chirality :  0.066   0.238   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/Z
  covalent geometry    : bond        0.01074 /  0.83 (12880)
  covalent geometry    : angle       1.11147 /  0.86 (18637)
  hydrogen bonds       : bond        0.14247 /  9.51 (  710)
  hydrogen bonds       : angle       4.96672 /  3.52 ( 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  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.7960 (pp30) cc_final: 0.7737 (pm20)
REVERT: A   96 GLU cc_start: 0.8131 (tp30) cc_final: 0.7900 (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: 0.8022 (m-10)
REVERT: C   56 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: C   75 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8641 (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: 0.7867 (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: 0.6772 (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: 0.8458 (t0)
REVERT: H   83 TYR cc_start: 0.8742 (m-10) cc_final: 0.8299 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1515
  time to fit residues: 46.6951
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  : 0.285 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 97 optimal weight:   20.0000
   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:    1.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 HIS
C  73 ASN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  67 ASN
H  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.085726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.058723 restraints weight = 39688.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.060553 restraints weight = 20145.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.061726 restraints weight = 13824.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.062415 restraints weight = 11242.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.062799 restraints weight = 10077.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  12880  Z= 0.165
  Angle     :  0.724   7.911  18637  Z= 0.420
  Chirality :  0.049   0.287   2114
  Planarity :  0.005   0.045   1347
  Dihedral  : 31.250 177.376   4019
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.14 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.37 (0.26), residues: 753
  helix: -0.35 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop : -1.95 (0.30), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  29 
 TYR   0.015   0.002   TYR D  40 
 PHE   0.008   0.001   PHE A  84 
 TRP   0.011   0.001   TRP V 530 
 HIS   0.006   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.17 (12880)
  covalent geometry    : angle       0.72443 /  0.42 (18637)
  hydrogen bonds       : bond        0.08004 /  5.29 (  710)
  hydrogen bonds       : angle       3.34508 /  2.41 ( 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
  233 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 218
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8140 (pp30) cc_final: 0.7777 (pm20)
REVERT: A   50 GLU cc_start: 0.8982 (tt0) cc_final: 0.8779 (tt0)
REVERT: A   96 GLU cc_start: 0.8529 (tp30) cc_final: 0.8271 (mm-30)
REVERT: A  107 GLU cc_start: 0.8365 (pt0) cc_final: 0.8018 (pt0)
REVERT: A  127 GLN cc_start: 0.8214 (tp-100) cc_final: 0.7986 (tp40)
REVERT: B   53 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8426 (tm-30)
REVERT: B   88 TYR cc_start: 0.8401 (m-10) cc_final: 0.8137 (m-10)
REVERT: B   91 LYS cc_start: 0.8916 (tttt) cc_final: 0.8269 (tptp)
REVERT: C   23 LEU cc_start: 0.9484 (mt) cc_final: 0.9113 (mp)
REVERT: C   56 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8601 (tm-30)
REVERT: C   57 TYR cc_start: 0.9248 (t80) cc_final: 0.8897 (t80)
REVERT: C   71 ARG cc_start: 0.8838 (ttm110) cc_final: 0.8398 (ttp80)
REVERT: C   75 LYS cc_start: 0.8716 (mmtp) cc_final: 0.8423 (mmtm)
REVERT: D   34 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8795 (ttpp)
REVERT: D   35 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6279 (mm-30)
REVERT: D   63 ASN cc_start: 0.8764 (t0) cc_final: 0.8534 (t0)
REVERT: D   67 ASN cc_start: 0.8857 (m-40) cc_final: 0.8237 (t0)
REVERT: D   68 ASP cc_start: 0.8555 (t70) cc_final: 0.8205 (t0)
REVERT: D   71 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: D   76 GLU cc_start: 0.8213 (tp30) cc_final: 0.7933 (tp30)
REVERT: D   83 TYR cc_start: 0.8691 (m-10) cc_final: 0.8450 (m-10)
REVERT: E   73 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: F   24 ASP cc_start: 0.8724 (t0) cc_final: 0.8506 (t0)
REVERT: F   64 ASN cc_start: 0.8967 (t0) cc_final: 0.8171 (t0)
REVERT: F   91 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8703 (ttpp)
REVERT: F   93 GLN cc_start: 0.7573 (mt0) cc_final: 0.6388 (mt0)
REVERT: G   64 GLU cc_start: 0.8954 (tp30) cc_final: 0.8477 (tp30)
REVERT: G   92 GLU cc_start: 0.7638 (tt0) cc_final: 0.5903 (pt0)
REVERT: H   42 TYR cc_start: 0.7864 (t80) cc_final: 0.7368 (t80)
REVERT: H   68 ASP cc_start: 0.9264 (t0) cc_final: 0.8769 (t0)
REVERT: H   71 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8611 (tm-30)
REVERT: H   76 GLU cc_start: 0.8346 (tp30) cc_final: 0.7773 (tp30)
REVERT: H   83 TYR cc_start: 0.8802 (m-10) cc_final: 0.8538 (m-80)
  outliers start: 15
  outliers final: 10
  residues processed: 220
  average time/residue: 0.1200
  time to fit residues: 35.9992
Evaluate side-chains
  199 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 189
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   82 THR
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain H residue   90 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 80 optimal weight:   20.0000
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 98 optimal weight:   30.0000
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 82 optimal weight:   30.0000
   chunk 35 optimal weight:    0.5980
   overall best weight:    1.9186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.085361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.058302 restraints weight = 40248.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.060098 restraints weight = 19926.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.061304 restraints weight = 13538.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.061937 restraints weight = 10920.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.062325 restraints weight = 9827.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12880  Z= 0.170
  Angle     :  0.684   8.428  18637  Z= 0.395
  Chirality :  0.046   0.267   2114
  Planarity :  0.004   0.046   1347
  Dihedral  : 31.256 176.305   4019
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 18.97 %
    Favored  : 77.90 %
  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: -0.15 (0.29), residues: 753
  helix:  0.67 (0.22), residues: 517
  sheet:  None (None), residues: 0
  loop : -1.78 (0.32), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  29 
 TYR   0.020   0.002   TYR F  98 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.009   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.17 (12880)
  covalent geometry    : angle       0.68351 /  0.39 (18637)
  hydrogen bonds       : bond        0.07216 /  4.75 (  710)
  hydrogen bonds       : angle       3.01031 /  2.15 ( 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
  221 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 201
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8165 (pp30) cc_final: 0.7784 (pm20)
REVERT: A   50 GLU cc_start: 0.8970 (tt0) cc_final: 0.8685 (tt0)
REVERT: A   56 LYS cc_start: 0.9230 (ttmm) cc_final: 0.9022 (ttmm)
REVERT: A   96 GLU cc_start: 0.8547 (tp30) cc_final: 0.8242 (mm-30)
REVERT: A  107 GLU cc_start: 0.8352 (pt0) cc_final: 0.7986 (pt0)
REVERT: A  127 GLN cc_start: 0.8322 (tp-100) cc_final: 0.8033 (tp40)
REVERT: B   53 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8400 (tm-30)
REVERT: B   84 MET cc_start: 0.7982 (tpp) cc_final: 0.7678 (tpp)
REVERT: B   88 TYR cc_start: 0.8397 (m-10) cc_final: 0.8114 (m-10)
REVERT: B   91 LYS cc_start: 0.8842 (tttt) cc_final: 0.8226 (tptp)
REVERT: C   23 LEU cc_start: 0.9454 (mt) cc_final: 0.9078 (mp)
REVERT: C   56 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8764 (tm-30)
REVERT: C   57 TYR cc_start: 0.9210 (t80) cc_final: 0.8896 (t80)
REVERT: C   71 ARG cc_start: 0.8933 (ttm110) cc_final: 0.8484 (ttp80)
REVERT: D   34 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8833 (ttpp)
REVERT: D   67 ASN cc_start: 0.8794 (m-40) cc_final: 0.8196 (t0)
REVERT: D   68 ASP cc_start: 0.8551 (t70) cc_final: 0.8224 (t0)
REVERT: D   71 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8148 (tm-30)
REVERT: D   76 GLU cc_start: 0.8201 (tp30) cc_final: 0.7979 (tp30)
REVERT: E   73 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: F   24 ASP cc_start: 0.8644 (t0) cc_final: 0.8350 (t0)
REVERT: F   64 ASN cc_start: 0.9067 (t0) cc_final: 0.8264 (t0)
REVERT: F   91 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8669 (ttpp)
REVERT: F   93 GLN cc_start: 0.7681 (mt0) cc_final: 0.6617 (mt0)
REVERT: G   64 GLU cc_start: 0.8935 (tp30) cc_final: 0.8489 (tp30)
REVERT: G   92 GLU cc_start: 0.6488 (tt0) cc_final: 0.6146 (tt0)
REVERT: H   42 TYR cc_start: 0.7899 (t80) cc_final: 0.7529 (t80)
REVERT: H   68 ASP cc_start: 0.9286 (t0) cc_final: 0.8790 (t0)
REVERT: H   83 TYR cc_start: 0.8762 (m-10) cc_final: 0.8230 (m-80)
  outliers start: 20
  outliers final: 12
  residues processed: 209
  average time/residue: 0.1142
  time to fit residues: 33.0064
Evaluate side-chains
  199 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 187
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue  135 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 92 optimal weight:   30.0000
   chunk 15 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 66 optimal weight:    0.3980
   chunk 21 optimal weight:    6.9990
   chunk 90 optimal weight:   30.0000
   chunk 41 optimal weight:    0.9990
   chunk 94 optimal weight:   20.0000
   chunk 73 optimal weight:   40.0000
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.086244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059186 restraints weight = 40386.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.061076 restraints weight = 20109.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.062276 restraints weight = 13647.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.062996 restraints weight = 11014.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.063385 restraints weight = 9817.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12880  Z= 0.149
  Angle     :  0.646   8.790  18637  Z= 0.376
  Chirality :  0.044   0.273   2114
  Planarity :  0.004   0.044   1347
  Dihedral  : 31.153 175.370   4019
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 21.32 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.53 (0.29), residues: 753
  helix:  1.18 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.49 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG V 522 
 TYR   0.019   0.002   TYR E 110 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.007   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.15 (12880)
  covalent geometry    : angle       0.64638 /  0.38 (18637)
  hydrogen bonds       : bond        0.06759 /  4.40 (  710)
  hydrogen bonds       : angle       2.79437 /  1.99 ( 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
  211 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 199
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8186 (pp30) cc_final: 0.7814 (pm20)
REVERT: A   50 GLU cc_start: 0.8951 (tt0) cc_final: 0.8671 (tt0)
REVERT: A  107 GLU cc_start: 0.8328 (pt0) cc_final: 0.7970 (pt0)
REVERT: A  127 GLN cc_start: 0.8361 (tp40) cc_final: 0.8006 (tp40)
REVERT: B   53 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8313 (tm-30)
REVERT: B   88 TYR cc_start: 0.8421 (m-10) cc_final: 0.8099 (m-10)
REVERT: B   91 LYS cc_start: 0.8758 (tttt) cc_final: 0.8162 (tptp)
REVERT: C   36 LYS cc_start: 0.9201 (mptt) cc_final: 0.8923 (mmtm)
REVERT: C   56 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8536 (tm-30)
REVERT: C   57 TYR cc_start: 0.9157 (t80) cc_final: 0.8831 (t80)
REVERT: C   71 ARG cc_start: 0.8939 (ttm110) cc_final: 0.8514 (ttp80)
REVERT: D   34 LYS cc_start: 0.9178 (mmmm) cc_final: 0.8292 (mptt)
REVERT: D   67 ASN cc_start: 0.8719 (m-40) cc_final: 0.8130 (t0)
REVERT: D   68 ASP cc_start: 0.8532 (t70) cc_final: 0.8235 (t0)
REVERT: D   71 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: E   73 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: F   24 ASP cc_start: 0.8608 (t0) cc_final: 0.8323 (t0)
REVERT: F   64 ASN cc_start: 0.9085 (t0) cc_final: 0.8243 (t0)
REVERT: F   88 TYR cc_start: 0.8635 (m-10) cc_final: 0.7854 (m-10)
REVERT: F   93 GLN cc_start: 0.7742 (mt0) cc_final: 0.6703 (mt0)
REVERT: G   64 GLU cc_start: 0.8940 (tp30) cc_final: 0.8462 (tp30)
REVERT: H   42 TYR cc_start: 0.7860 (t80) cc_final: 0.7530 (t80)
REVERT: H   68 ASP cc_start: 0.9275 (t0) cc_final: 0.8776 (t0)
REVERT: H   76 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7579 (tp30)
  outliers start: 12
  outliers final: 9
  residues processed: 204
  average time/residue: 0.1014
  time to fit residues: 29.1169
Evaluate side-chains
  199 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 190
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue  135 LEU
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:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 90 optimal weight:   30.0000
   chunk 34 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 79 optimal weight:   30.0000
   chunk 99 optimal weight:   40.0000
   chunk 47 optimal weight:    9.9990
   chunk 78 optimal weight:   30.0000
   chunk 85 optimal weight:   40.0000
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  59 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 = 0.085787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.058657 restraints weight = 40318.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.060445 restraints weight = 20259.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.061637 restraints weight = 13812.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.062323 restraints weight = 11155.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.062549 restraints weight = 9967.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12880  Z= 0.169
  Angle     :  0.649   7.254  18637  Z= 0.375
  Chirality :  0.043   0.269   2114
  Planarity :  0.004   0.043   1347
  Dihedral  : 31.057 175.049   4019
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.98 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.78 (0.30), residues: 753
  helix:  1.42 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.54 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  99 
 TYR   0.031   0.002   TYR D  83 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.007   0.001   TRP V 530 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.17 (12880)
  covalent geometry    : angle       0.64939 /  0.37 (18637)
  hydrogen bonds       : bond        0.06712 /  4.38 (  710)
  hydrogen bonds       : angle       2.83258 /  2.02 ( 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
  205 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 191
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8232 (pp30) cc_final: 0.7844 (pm20)
REVERT: A  107 GLU cc_start: 0.8321 (pt0) cc_final: 0.7973 (pt0)
REVERT: A  127 GLN cc_start: 0.8473 (tp40) cc_final: 0.8092 (tp40)
REVERT: B   53 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: B   91 LYS cc_start: 0.8766 (tttt) cc_final: 0.8187 (tptp)
REVERT: C   41 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: C   56 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: C   57 TYR cc_start: 0.9178 (t80) cc_final: 0.8840 (t80)
REVERT: C   71 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8673 (ttp80)
REVERT: D   34 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8310 (mptt)
REVERT: D   67 ASN cc_start: 0.8718 (m-40) cc_final: 0.8137 (t0)
REVERT: D   68 ASP cc_start: 0.8548 (t70) cc_final: 0.8258 (t0)
REVERT: D   71 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: E   73 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: F   24 ASP cc_start: 0.8616 (t0) cc_final: 0.8336 (t0)
REVERT: F   64 ASN cc_start: 0.9085 (t0) cc_final: 0.8232 (t0)
REVERT: F   88 TYR cc_start: 0.8430 (m-10) cc_final: 0.7987 (m-10)
REVERT: F   93 GLN cc_start: 0.7880 (mt0) cc_final: 0.6823 (mt0)
REVERT: G   64 GLU cc_start: 0.8966 (tp30) cc_final: 0.8492 (tp30)
REVERT: G  111 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6283 (pt)
REVERT: H   42 TYR cc_start: 0.7871 (t80) cc_final: 0.7618 (t80)
REVERT: H   68 ASP cc_start: 0.9277 (t0) cc_final: 0.8791 (t0)
REVERT: H   76 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7665 (tp30)
REVERT: H   83 TYR cc_start: 0.8635 (m-80) cc_final: 0.7924 (m-80)
REVERT: H   93 GLU cc_start: 0.8708 (mp0) cc_final: 0.8447 (mp0)
  outliers start: 14
  outliers final: 12
  residues processed: 197
  average time/residue: 0.1111
  time to fit residues: 30.7315
Evaluate side-chains
  195 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 182
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue  135 LEU
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:   30.0000
   chunk 61 optimal weight:    1.9990
   chunk 88 optimal weight:   30.0000
   chunk 98 optimal weight:   30.0000
   chunk 94 optimal weight:   30.0000
   chunk 12 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.086695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.059777 restraints weight = 40233.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.061668 restraints weight = 19928.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.062882 restraints weight = 13481.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.063588 restraints weight = 10855.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.063989 restraints weight = 9683.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053  12880  Z= 0.142
  Angle     :  0.623   9.381  18637  Z= 0.364
  Chirality :  0.042   0.277   2114
  Planarity :  0.004   0.055   1347
  Dihedral  : 30.929 174.234   4019
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.51 %
    Favored  : 73.51 %
  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:  1.10 (0.30), residues: 753
  helix:  1.66 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.39 (0.35), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG V 522 
 TYR   0.030   0.002   TYR D  83 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.004   0.001   TRP V 530 
 HIS   0.016   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.14 (12880)
  covalent geometry    : angle       0.62302 /  0.36 (18637)
  hydrogen bonds       : bond        0.06511 /  4.22 (  710)
  hydrogen bonds       : angle       2.67690 /  1.92 ( 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
  213 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 194
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8222 (pp30) cc_final: 0.7877 (pm20)
REVERT: A  107 GLU cc_start: 0.8298 (pt0) cc_final: 0.7960 (pt0)
REVERT: A  127 GLN cc_start: 0.8482 (tp40) cc_final: 0.8062 (tp40)
REVERT: B   53 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8638 (tm-30)
REVERT: B   91 LYS cc_start: 0.8735 (tttt) cc_final: 0.8165 (tptp)
REVERT: C   56 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8521 (tm-30)
REVERT: C   57 TYR cc_start: 0.9119 (t80) cc_final: 0.8787 (t80)
REVERT: C   71 ARG cc_start: 0.8966 (ttm110) cc_final: 0.8718 (ttp80)
REVERT: D   34 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8325 (mptt)
REVERT: D   67 ASN cc_start: 0.8651 (m-40) cc_final: 0.8067 (t0)
REVERT: D   68 ASP cc_start: 0.8516 (t70) cc_final: 0.8240 (t0)
REVERT: D   71 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8180 (tm-30)
REVERT: E   73 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: F   24 ASP cc_start: 0.8623 (t0) cc_final: 0.8404 (t0)
REVERT: F   64 ASN cc_start: 0.9121 (t0) cc_final: 0.8230 (t0)
REVERT: F   93 GLN cc_start: 0.7841 (mt0) cc_final: 0.6857 (mt0)
REVERT: G   24 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8012 (mp10)
REVERT: G   64 GLU cc_start: 0.8923 (tp30) cc_final: 0.8445 (tp30)
REVERT: G   92 GLU cc_start: 0.5881 (tt0) cc_final: 0.5050 (pt0)
REVERT: G  111 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6222 (pt)
REVERT: H   42 TYR cc_start: 0.7824 (t80) cc_final: 0.7552 (t80)
REVERT: H   68 ASP cc_start: 0.9245 (t0) cc_final: 0.8748 (t0)
REVERT: H   76 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7636 (tp30)
REVERT: H   83 TYR cc_start: 0.8628 (m-80) cc_final: 0.8050 (m-80)
REVERT: H   93 GLU cc_start: 0.8723 (mp0) cc_final: 0.8457 (mp0)
REVERT: H  105 GLU cc_start: 0.7863 (pm20) cc_final: 0.7462 (pm20)
  outliers start: 19
  outliers final: 12
  residues processed: 205
  average time/residue: 0.1123
  time to fit residues: 32.3725
Evaluate side-chains
  196 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 183
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain E residue  135 LEU
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:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 9 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 77 optimal weight:   30.0000
   chunk 43 optimal weight:    4.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  82 HIS
F  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.086006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.058574 restraints weight = 40154.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.060437 restraints weight = 19416.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.061686 restraints weight = 13024.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.062406 restraints weight = 10418.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.062797 restraints weight = 9262.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12880  Z= 0.168
  Angle     :  0.636   7.165  18637  Z= 0.371
  Chirality :  0.042   0.273   2114
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.904 173.680   4019
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 24.61 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.16 (0.30), residues: 753
  helix:  1.69 (0.23), residues: 517
  sheet:  None (None), residues: 0
  loop : -1.35 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG V 522 
 TYR   0.049   0.002   TYR B  88 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.005   0.001   TRP V 530 
 HIS   0.010   0.001   HIS D  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.17 (12880)
  covalent geometry    : angle       0.63563 /  0.37 (18637)
  hydrogen bonds       : bond        0.06516 /  4.24 (  710)
  hydrogen bonds       : angle       2.75003 /  1.96 ( 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
  209 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 187
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8243 (pp30) cc_final: 0.7878 (pm20)
REVERT: A   50 GLU cc_start: 0.8967 (tt0) cc_final: 0.8716 (tt0)
REVERT: A  107 GLU cc_start: 0.8310 (pt0) cc_final: 0.7978 (pt0)
REVERT: A  127 GLN cc_start: 0.8512 (tp40) cc_final: 0.8084 (tp40)
REVERT: B   53 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8645 (tm-30)
REVERT: B   91 LYS cc_start: 0.8766 (tttt) cc_final: 0.8194 (tptp)
REVERT: B   92 ARG cc_start: 0.8682 (tmm160) cc_final: 0.7885 (tmm160)
REVERT: C   56 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8544 (tm-30)
REVERT: C   57 TYR cc_start: 0.9140 (t80) cc_final: 0.8652 (t80)
REVERT: C   61 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: C   71 ARG cc_start: 0.8970 (ttm110) cc_final: 0.8679 (ttp80)
REVERT: D   34 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8335 (mptt)
REVERT: D   67 ASN cc_start: 0.8672 (m-40) cc_final: 0.8065 (t0)
REVERT: D   68 ASP cc_start: 0.8532 (t70) cc_final: 0.8272 (t0)
REVERT: D   71 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: E   73 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: F   24 ASP cc_start: 0.8654 (t0) cc_final: 0.8422 (t0)
REVERT: F   64 ASN cc_start: 0.9127 (t0) cc_final: 0.8464 (t0)
REVERT: G   24 GLN cc_start: 0.8647 (mm-40) cc_final: 0.7978 (mp10)
REVERT: G   64 GLU cc_start: 0.8962 (tp30) cc_final: 0.8482 (tp30)
REVERT: G   92 GLU cc_start: 0.5864 (tt0) cc_final: 0.5032 (pt0)
REVERT: G  111 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6253 (pt)
REVERT: H   42 TYR cc_start: 0.7825 (t80) cc_final: 0.7580 (t80)
REVERT: H   68 ASP cc_start: 0.9255 (t0) cc_final: 0.8790 (t0)
REVERT: H   76 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7654 (tp30)
REVERT: H  105 GLU cc_start: 0.7736 (pm20) cc_final: 0.7203 (pm20)
  outliers start: 22
  outliers final: 13
  residues processed: 199
  average time/residue: 0.1107
  time to fit residues: 31.3380
Evaluate side-chains
  194 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue  135 LEU
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:   30.0000
   chunk 15 optimal weight:    2.9990
   chunk 83 optimal weight:   30.0000
   chunk 69 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 94 optimal weight:   30.0000
   chunk 36 optimal weight:    0.0770
   chunk 45 optimal weight:   10.0000
   overall best weight:    1.6144

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.085565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.059159 restraints weight = 40240.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.061045 restraints weight = 19455.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.062242 restraints weight = 12932.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.062985 restraints weight = 10296.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.063382 restraints weight = 9087.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12880  Z= 0.152
  Angle     :  0.621   8.326  18637  Z= 0.364
  Chirality :  0.041   0.278   2114
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.876 172.602   4019
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 26.96 %
    Favored  : 70.69 %
  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:  1.24 (0.30), residues: 753
  helix:  1.76 (0.23), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.38 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  35 
 TYR   0.053   0.003   TYR D  83 
 PHE   0.042   0.002   PHE A  84 
 TRP   0.004   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.15 (12880)
  covalent geometry    : angle       0.62142 /  0.36 (18637)
  hydrogen bonds       : bond        0.06422 /  4.16 (  710)
  hydrogen bonds       : angle       2.66533 /  1.90 ( 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
  198 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 183
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8242 (pp30) cc_final: 0.7881 (pm20)
REVERT: A   50 GLU cc_start: 0.8954 (tt0) cc_final: 0.8690 (tt0)
REVERT: A  107 GLU cc_start: 0.8297 (pt0) cc_final: 0.7975 (pt0)
REVERT: A  127 GLN cc_start: 0.8535 (tp40) cc_final: 0.8098 (tp40)
REVERT: B   53 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8619 (tm-30)
REVERT: B   91 LYS cc_start: 0.8792 (tttt) cc_final: 0.8234 (tptp)
REVERT: B   92 ARG cc_start: 0.8704 (tmm160) cc_final: 0.7909 (tmm160)
REVERT: C   41 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7607 (mm-30)
REVERT: C   56 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: C   57 TYR cc_start: 0.9151 (t80) cc_final: 0.8658 (t80)
REVERT: C   61 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8282 (tm-30)
REVERT: C   71 ARG cc_start: 0.8952 (ttm110) cc_final: 0.8676 (ttp80)
REVERT: D   34 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8375 (mptt)
REVERT: D   35 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7545 (mm-30)
REVERT: D   68 ASP cc_start: 0.8501 (t70) cc_final: 0.8097 (t0)
REVERT: D   71 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: E   73 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8167 (tm-30)
REVERT: F   64 ASN cc_start: 0.9104 (t0) cc_final: 0.8457 (t0)
REVERT: F   88 TYR cc_start: 0.8647 (m-10) cc_final: 0.7948 (m-10)
REVERT: G   24 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8156 (mp10)
REVERT: G   64 GLU cc_start: 0.8930 (tp30) cc_final: 0.8460 (tp30)
REVERT: G   92 GLU cc_start: 0.5879 (tt0) cc_final: 0.4799 (pt0)
REVERT: G  111 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6258 (pt)
REVERT: H   42 TYR cc_start: 0.7834 (t80) cc_final: 0.7585 (t80)
REVERT: H   68 ASP cc_start: 0.9224 (t0) cc_final: 0.8753 (t0)
REVERT: H   76 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7590 (tp30)
REVERT: H   83 TYR cc_start: 0.8456 (m-80) cc_final: 0.8138 (m-80)
REVERT: H  105 GLU cc_start: 0.7832 (pm20) cc_final: 0.7287 (pm20)
  outliers start: 15
  outliers final: 11
  residues processed: 191
  average time/residue: 0.1153
  time to fit residues: 30.9219
Evaluate side-chains
  192 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 180
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue  135 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:   30.0000
   chunk 16 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 90 optimal weight:   30.0000
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0270
   chunk 31 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.1442

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.086030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.059953 restraints weight = 40306.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.061803 restraints weight = 19372.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.063023 restraints weight = 12806.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.063762 restraints weight = 10171.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.064135 restraints weight = 8959.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12880  Z= 0.145
  Angle     :  0.620   7.090  18637  Z= 0.366
  Chirality :  0.040   0.276   2114
  Planarity :  0.004   0.045   1347
  Dihedral  : 30.826 171.804   4019
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 29.15 %
    Favored  : 68.81 %
  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:  1.24 (0.30), residues: 753
  helix:  1.76 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.40 (0.36), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  23 
 TYR   0.059   0.003   TYR B  88 
 PHE   0.025   0.001   PHE E  84 
 TRP   0.004   0.001   TRP E  47 
 HIS   0.006   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.15 (12880)
  covalent geometry    : angle       0.62028 /  0.37 (18637)
  hydrogen bonds       : bond        0.06366 /  4.11 (  710)
  hydrogen bonds       : angle       2.62998 /  1.88 ( 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
  206 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 193
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8238 (pp30) cc_final: 0.7891 (pm20)
REVERT: A  104 HIS cc_start: 0.7699 (m90) cc_final: 0.7414 (t70)
REVERT: A  127 GLN cc_start: 0.8529 (tp40) cc_final: 0.8078 (tp40)
REVERT: B   53 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8561 (tm-30)
REVERT: B   91 LYS cc_start: 0.8770 (tttt) cc_final: 0.8296 (tptp)
REVERT: B   92 ARG cc_start: 0.8628 (tmm160) cc_final: 0.7766 (tmm160)
REVERT: C   41 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7653 (mm-30)
REVERT: C   56 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8507 (tm-30)
REVERT: C   57 TYR cc_start: 0.9124 (t80) cc_final: 0.8638 (t80)
REVERT: C   61 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8293 (tm-30)
REVERT: C   71 ARG cc_start: 0.8955 (ttm110) cc_final: 0.8642 (ttp80)
REVERT: D   34 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8369 (mptt)
REVERT: D   35 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7548 (mm-30)
REVERT: D   68 ASP cc_start: 0.8474 (t70) cc_final: 0.8067 (t0)
REVERT: D   71 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8233 (tm-30)
REVERT: E   73 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: F   64 ASN cc_start: 0.9124 (t0) cc_final: 0.8483 (t0)
REVERT: F   88 TYR cc_start: 0.8619 (m-10) cc_final: 0.7797 (m-10)
REVERT: G   24 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8178 (mp10)
REVERT: G   64 GLU cc_start: 0.8926 (tp30) cc_final: 0.8484 (tp30)
REVERT: G   92 GLU cc_start: 0.5887 (tt0) cc_final: 0.4806 (pt0)
REVERT: G  111 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6237 (pt)
REVERT: H   42 TYR cc_start: 0.7831 (t80) cc_final: 0.7618 (t80)
REVERT: H   68 ASP cc_start: 0.9209 (t0) cc_final: 0.8746 (t0)
REVERT: H   76 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7571 (tp30)
REVERT: H   83 TYR cc_start: 0.8445 (m-80) cc_final: 0.8089 (m-80)
REVERT: H  105 GLU cc_start: 0.7917 (pm20) cc_final: 0.7378 (pm20)
  outliers start: 13
  outliers final: 9
  residues processed: 199
  average time/residue: 0.1115
  time to fit residues: 31.4746
Evaluate side-chains
  197 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 187
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue  104 HIS
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue  111 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:   30.0000
   chunk 41 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 73 optimal weight:   40.0000
   chunk 68 optimal weight:    7.9990
   chunk 22 optimal weight:    8.9990
   chunk 72 optimal weight:   50.0000
   chunk 30 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 80 optimal weight:   30.0000
   chunk 26 optimal weight:    0.3980
   overall best weight:    2.8386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.085012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.058615 restraints weight = 40510.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.060499 restraints weight = 19653.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.061697 restraints weight = 13100.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.062410 restraints weight = 10449.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.062775 restraints weight = 9248.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.3031

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= 0.190
  Angle     :  0.651   7.031  18637  Z= 0.379
  Chirality :  0.041   0.273   2114
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.856 170.759   4019
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 28.06 %
    Favored  : 69.28 %
  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:  1.17 (0.30), residues: 753
  helix:  1.68 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.36 (0.36), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  71 
 TYR   0.097   0.003   TYR D  83 
 PHE   0.016   0.001   PHE A  84 
 TRP   0.005   0.001   TRP V 530 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.19 (12880)
  covalent geometry    : angle       0.65122 /  0.38 (18637)
  hydrogen bonds       : bond        0.06542 /  4.25 (  710)
  hydrogen bonds       : angle       2.77421 /  1.98 ( 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
  198 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 0.313 
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: 0.7891 (pm20)
REVERT: A  107 GLU cc_start: 0.8283 (pt0) cc_final: 0.7964 (pt0)
REVERT: A  127 GLN cc_start: 0.8554 (tp40) cc_final: 0.8118 (tp40)
REVERT: B   53 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8645 (tm-30)
REVERT: B   91 LYS cc_start: 0.8799 (tttt) cc_final: 0.8316 (tptp)
REVERT: B   92 ARG cc_start: 0.8693 (tmm160) cc_final: 0.7777 (tmm160)
REVERT: C   42 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.8012 (mmm-85)
REVERT: C   56 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8533 (tm-30)
REVERT: C   57 TYR cc_start: 0.9186 (t80) cc_final: 0.8674 (t80)
REVERT: C   61 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8317 (tm-30)
REVERT: C   63 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9052 (mm)
REVERT: C   71 ARG cc_start: 0.8983 (ttm110) cc_final: 0.8668 (ttp80)
REVERT: D   34 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8352 (mptt)
REVERT: D   68 ASP cc_start: 0.8533 (t70) cc_final: 0.8130 (t0)
REVERT: D   71 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8250 (tm-30)
REVERT: E   73 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8187 (tm-30)
REVERT: F   64 ASN cc_start: 0.9120 (t0) cc_final: 0.8465 (t0)
REVERT: F   79 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8704 (mtpp)
REVERT: F   88 TYR cc_start: 0.8640 (m-10) cc_final: 0.7967 (m-10)
REVERT: G   24 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8129 (mp10)
REVERT: G   64 GLU cc_start: 0.8947 (tp30) cc_final: 0.8497 (tp30)
REVERT: G   92 GLU cc_start: 0.6043 (tt0) cc_final: 0.5363 (pt0)
REVERT: G  111 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6324 (pt)
REVERT: H   42 TYR cc_start: 0.7836 (t80) cc_final: 0.7565 (t80)
REVERT: H   68 ASP cc_start: 0.9240 (t0) cc_final: 0.8775 (t0)
REVERT: H   76 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7684 (tp30)
REVERT: H   83 TYR cc_start: 0.8545 (m-80) cc_final: 0.8143 (m-80)
REVERT: H  105 GLU cc_start: 0.7918 (pm20) cc_final: 0.7386 (pm20)
REVERT: V  522 ARG cc_start: 0.4176 (ptm160) cc_final: 0.3950 (ptm160)
  outliers start: 17
  outliers final: 11
  residues processed: 191
  average time/residue: 0.1143
  time to fit residues: 30.5248
Evaluate side-chains
  192 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 179
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
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   74 LYS
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue  111 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:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 89 optimal weight:   30.0000
   chunk 54 optimal weight:    7.9990
   chunk 77 optimal weight:   30.0000
   chunk 11 optimal weight:    3.9990
   chunk 99 optimal weight:   40.0000
   chunk 19 optimal weight:    1.9990
   chunk 85 optimal weight:   40.0000
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.084752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.058500 restraints weight = 40334.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.060374 restraints weight = 19546.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.061567 restraints weight = 12989.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.062279 restraints weight = 10370.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.062671 restraints weight = 9165.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3079

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= 0.194
  Angle     :  0.663   9.087  18637  Z= 0.385
  Chirality :  0.041   0.276   2114
  Planarity :  0.004   0.052   1347
  Dihedral  : 30.840 169.649   4019
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 29.00 %
    Favored  : 68.65 %
  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:  1.11 (0.30), residues: 753
  helix:  1.63 (0.23), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.32 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  71 
 TYR   0.116   0.003   TYR D  83 
 PHE   0.014   0.001   PHE E  84 
 TRP   0.004   0.001   TRP V 530 
 HIS   0.008   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.19 (12880)
  covalent geometry    : angle       0.66259 /  0.38 (18637)
  hydrogen bonds       : bond        0.06532 /  4.24 (  710)
  hydrogen bonds       : angle       2.85901 /  2.04 ( 1730)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1869.51 seconds
wall clock time: 32 minutes 58.39 seconds (1978.39 seconds total)