Starting phenix.real_space_refine
on Tue Jul 29 20:13:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6se6_10152/07_2025/6se6_10152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6se6_10152/07_2025/6se6_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_10152/07_2025/6se6_10152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6se6_10152/07_2025/6se6_10152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6se6_10152/07_2025/6se6_10152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6se6_10152/07_2025/6se6_10152.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.48, per 1000 atoms: 0.62
  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: 2.81
  Conformation dependent library (CDL) restraints added in 881.0 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: 5.97
  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: 4.64

  Time building geometry restraints manager: 3.36 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2460
        2.78 -     3.31: 10073
        3.31 -     3.84: 24303
        3.84 -     4.37: 27108
        4.37 -     4.90: 38480
  Nonbonded interactions: 102424
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  -4 "
            pdb=" N2   DG J   4 "
     model   vdw
     2.247 2.496
  nonbonded pdb=" O2   DC I -62 "
            pdb=" N2   DG J  62 "
     model   vdw
     2.249 2.496
  nonbonded pdb=" O2   DC I -56 "
            pdb=" N2   DG J  56 "
     model   vdw
     2.264 2.496
  nonbonded pdb=" N2   DG I -60 "
            pdb=" O2   DC J  60 "
     model   vdw
     2.268 2.496
  nonbonded pdb=" O2   DC I   5 "
            pdb=" N2   DG J  -5 "
     model   vdw
     2.275 2.496
  ... (remaining 102419 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 21 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 116)
}
ncs_group {
  reference = (chain 'D' and resid 35 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     33.330
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.095  12880  Z= 0.448
  Angle     :  0.998  12.172  18637  Z= 0.571
  Chirality :  0.059   0.233   2114
  Planarity :  0.008   0.074   1347
  Dihedral  : 27.962 178.630   5528
  Min Nonbonded Distance : 2.247

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

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.016   0.002   TRP V 530 
 HIS   0.015   0.002   HIS F  75 
 PHE   0.016   0.003   PHE A  84 
 TYR   0.022   0.003   TYR G  50 
 ARG   0.008   0.001   ARG E 133 

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

*********************** 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  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.7960 (pp30) cc_final: 0.7738 (pm20)
REVERT: A   96 GLU cc_start: 0.8131 (tp30) cc_final: 0.7898 (mm-30)
REVERT: B   53 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8414 (tm-30)
REVERT: B   88 TYR cc_start: 0.8395 (m-10) cc_final: 0.8023 (m-10)
REVERT: C   56 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8308 (tm-30)
REVERT: C   75 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8644 (mmtm)
REVERT: D   59 MET cc_start: 0.8838 (tpp) cc_final: 0.8635 (tpp)
REVERT: D   63 ASN cc_start: 0.8898 (t0) cc_final: 0.8215 (t0)
REVERT: D   67 ASN cc_start: 0.8841 (m-40) cc_final: 0.8383 (t0)
REVERT: D   68 ASP cc_start: 0.8095 (t70) cc_final: 0.7869 (t0)
REVERT: D   71 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: D   76 GLU cc_start: 0.8063 (tp30) cc_final: 0.7842 (tp30)
REVERT: E   73 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7548 (tm-30)
REVERT: F   64 ASN cc_start: 0.8302 (t0) cc_final: 0.7761 (t0)
REVERT: F   88 TYR cc_start: 0.8906 (m-10) cc_final: 0.7888 (m-10)
REVERT: F   91 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8898 (ttpp)
REVERT: F   93 GLN cc_start: 0.7584 (mt0) cc_final: 0.6771 (mt0)
REVERT: G   64 GLU cc_start: 0.8568 (tp30) cc_final: 0.8344 (tp30)
REVERT: H   42 TYR cc_start: 0.7781 (t80) cc_final: 0.7298 (t80)
REVERT: H   68 ASP cc_start: 0.8689 (t0) cc_final: 0.8459 (t0)
REVERT: H   83 TYR cc_start: 0.8742 (m-10) cc_final: 0.8298 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.3591
  time to fit residues: 109.0131
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  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 76 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    1.5786

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.086200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.059134 restraints weight = 39291.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.060939 restraints weight = 19935.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.062116 restraints weight = 13676.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12880  Z= 0.181
  Angle     :  0.615   6.486  18637  Z= 0.365
  Chirality :  0.034   0.175   2114
  Planarity :  0.004   0.045   1347
  Dihedral  : 30.776 175.387   4019
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.55 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.27), residues: 753
  helix:  0.03 (0.21), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.69 (0.32), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.009   0.001   PHE A  84 
 TYR   0.016   0.002   TYR D  40 
 ARG   0.006   0.001   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06506 (  710)
  hydrogen bonds       : angle       2.95258 ( 1730)
  covalent geometry    : bond        0.00397 (12880)
  covalent geometry    : angle       0.61535 (18637)

*********************** 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
  228 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 218
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8185 (pp30) cc_final: 0.7776 (pm20)
REVERT: A  107 GLU cc_start: 0.8341 (pt0) cc_final: 0.8057 (pt0)
REVERT: A  127 GLN cc_start: 0.8317 (tp40) cc_final: 0.8029 (tp40)
REVERT: B   53 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8353 (tm-30)
REVERT: B   88 TYR cc_start: 0.8459 (m-10) cc_final: 0.8163 (m-10)
REVERT: B   91 LYS cc_start: 0.8878 (tttt) cc_final: 0.8234 (tptp)
REVERT: C   36 LYS cc_start: 0.9252 (mptt) cc_final: 0.8996 (mmtm)
REVERT: C   56 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8577 (tm-30)
REVERT: C   57 TYR cc_start: 0.9191 (t80) cc_final: 0.8886 (t80)
REVERT: C   61 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8275 (tm-30)
REVERT: C   71 ARG cc_start: 0.8923 (ttm110) cc_final: 0.8505 (ttp80)
REVERT: D   34 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8278 (mptt)
REVERT: D   67 ASN cc_start: 0.8818 (m-40) cc_final: 0.8209 (t0)
REVERT: D   68 ASP cc_start: 0.8558 (t70) cc_final: 0.8261 (t0)
REVERT: D   71 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: E   73 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: F   64 ASN cc_start: 0.9052 (t0) cc_final: 0.8313 (t0)
REVERT: F   91 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8744 (ttpp)
REVERT: F   93 GLN cc_start: 0.7770 (mt0) cc_final: 0.6799 (mt0)
REVERT: G   64 GLU cc_start: 0.8952 (tp30) cc_final: 0.8354 (tp30)
REVERT: G   92 GLU cc_start: 0.7004 (tt0) cc_final: 0.6492 (tt0)
REVERT: H   42 TYR cc_start: 0.7914 (t80) cc_final: 0.7454 (t80)
REVERT: H   68 ASP cc_start: 0.9271 (t0) cc_final: 0.8789 (t0)
REVERT: H   83 TYR cc_start: 0.8770 (m-10) cc_final: 0.8168 (m-80)
REVERT: H   93 GLU cc_start: 0.8861 (mp0) cc_final: 0.8622 (mp0)
  outliers start: 10
  outliers final: 6
  residues processed: 220
  average time/residue: 0.2848
  time to fit residues: 83.8124
Evaluate side-chains
  193 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 187
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   72 ASP
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0170
   chunk 36 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   overall best weight:    1.0020

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.087263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.060451 restraints weight = 40533.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.062342 restraints weight = 20065.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.063585 restraints weight = 13550.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12880  Z= 0.161
  Angle     :  0.579   9.058  18637  Z= 0.344
  Chirality :  0.033   0.167   2114
  Planarity :  0.004   0.043   1347
  Dihedral  : 30.509 174.892   4019
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.44 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.29), residues: 753
  helix:  1.12 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.50 (0.34), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.008   0.001   PHE A  78 
 TYR   0.020   0.001   TYR D  83 
 ARG   0.008   0.000   ARG C  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06029 (  710)
  hydrogen bonds       : angle       2.64421 ( 1730)
  covalent geometry    : bond        0.00351 (12880)
  covalent geometry    : angle       0.57934 (18637)

*********************** 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
  219 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 206
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8263 (pp30) cc_final: 0.7883 (pm20)
REVERT: A   87 GLN cc_start: 0.8378 (mt0) cc_final: 0.8159 (mt0)
REVERT: A  104 HIS cc_start: 0.7741 (m90) cc_final: 0.7431 (t70)
REVERT: B   53 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: B   91 LYS cc_start: 0.8784 (tttt) cc_final: 0.8250 (tptp)
REVERT: B   92 ARG cc_start: 0.8636 (tmm160) cc_final: 0.7937 (tmm160)
REVERT: C   36 LYS cc_start: 0.9210 (mptt) cc_final: 0.8951 (mmtm)
REVERT: C   56 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8455 (tm-30)
REVERT: C   57 TYR cc_start: 0.9080 (t80) cc_final: 0.8784 (t80)
REVERT: C   71 ARG cc_start: 0.8944 (ttm110) cc_final: 0.8651 (ttp80)
REVERT: D   34 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8351 (mptt)
REVERT: D   35 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7013 (mm-30)
REVERT: D   67 ASN cc_start: 0.8677 (m-40) cc_final: 0.8089 (t0)
REVERT: D   71 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8184 (tm-30)
REVERT: E   73 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8148 (tm-30)
REVERT: F   24 ASP cc_start: 0.8814 (t0) cc_final: 0.8565 (t0)
REVERT: F   64 ASN cc_start: 0.9143 (t0) cc_final: 0.8504 (t0)
REVERT: F   88 TYR cc_start: 0.8569 (m-10) cc_final: 0.7823 (m-10)
REVERT: F   91 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8654 (ttpp)
REVERT: G   24 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8132 (mp10)
REVERT: G   51 MET cc_start: 0.8838 (tpp) cc_final: 0.8619 (tpp)
REVERT: G   81 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7857 (tpt170)
REVERT: H   42 TYR cc_start: 0.7799 (t80) cc_final: 0.7525 (t80)
REVERT: H   68 ASP cc_start: 0.9247 (t0) cc_final: 0.8762 (t0)
REVERT: H   93 GLU cc_start: 0.8834 (mp0) cc_final: 0.8587 (mp0)
  outliers start: 13
  outliers final: 9
  residues processed: 211
  average time/residue: 0.2694
  time to fit residues: 77.5723
Evaluate side-chains
  198 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 189
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  100 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 97 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 98 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** 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 = 0.085031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.057781 restraints weight = 39955.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.059578 restraints weight = 20170.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.060744 restraints weight = 13829.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12880  Z= 0.242
  Angle     :  0.621   5.744  18637  Z= 0.363
  Chirality :  0.036   0.165   2114
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.643 171.959   4019
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 21.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.30), residues: 753
  helix:  1.37 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.35 (0.35), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP V 530 
 HIS   0.008   0.001   HIS F  75 
 PHE   0.010   0.001   PHE E  84 
 TYR   0.035   0.002   TYR B  88 
 ARG   0.007   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06307 (  710)
  hydrogen bonds       : angle       2.90910 ( 1730)
  covalent geometry    : bond        0.00546 (12880)
  covalent geometry    : angle       0.62116 (18637)

*********************** 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
  213 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 184
  time to evaluate  : 0.903 
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: 0.7894 (pm20)
REVERT: A  107 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7990 (pt0)
REVERT: B   53 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8783 (tm-30)
REVERT: B   91 LYS cc_start: 0.8838 (tttt) cc_final: 0.8269 (tptp)
REVERT: C   36 LYS cc_start: 0.9217 (mptt) cc_final: 0.8977 (mmtm)
REVERT: C   56 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8766 (tm-30)
REVERT: C   71 ARG cc_start: 0.8983 (ttm110) cc_final: 0.8625 (ttp80)
REVERT: C  104 GLN cc_start: 0.8773 (mp10) cc_final: 0.8133 (mp10)
REVERT: D   34 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8404 (mptt)
REVERT: D   67 ASN cc_start: 0.8717 (m-40) cc_final: 0.8164 (t0)
REVERT: D   68 ASP cc_start: 0.8606 (t70) cc_final: 0.8337 (t0)
REVERT: D   71 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: E   53 LYS cc_start: 0.9287 (tppp) cc_final: 0.8948 (tppt)
REVERT: E   73 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: F   24 ASP cc_start: 0.8762 (t0) cc_final: 0.8532 (t0)
REVERT: F   64 ASN cc_start: 0.9150 (t0) cc_final: 0.8522 (t0)
REVERT: F   91 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8680 (ttpp)
REVERT: G   24 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8117 (mp10)
REVERT: H   42 TYR cc_start: 0.7825 (t80) cc_final: 0.7600 (t80)
REVERT: H   68 ASP cc_start: 0.9308 (t0) cc_final: 0.8860 (t0)
REVERT: H   83 TYR cc_start: 0.8771 (m-80) cc_final: 0.8226 (m-80)
  outliers start: 29
  outliers final: 21
  residues processed: 195
  average time/residue: 0.2566
  time to fit residues: 69.2588
Evaluate side-chains
  200 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 178
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain 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 39 optimal weight:    6.9990
   chunk 94 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 88 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   chunk 60 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  75 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.084683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.057263 restraints weight = 40123.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.059176 restraints weight = 19388.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.060386 restraints weight = 12994.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  12880  Z= 0.247
  Angle     :  0.627   7.395  18637  Z= 0.366
  Chirality :  0.036   0.162   2114
  Planarity :  0.004   0.042   1347
  Dihedral  : 30.697 169.901   4019
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 23.82 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.30), residues: 753
  helix:  1.47 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -1.22 (0.35), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP V 530 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.037   0.002   TYR B  88 
 ARG   0.005   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06247 (  710)
  hydrogen bonds       : angle       2.97079 ( 1730)
  covalent geometry    : bond        0.00558 (12880)
  covalent geometry    : angle       0.62737 (18637)

*********************** 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
  210 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 182
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8207 (pp30) cc_final: 0.7830 (pm20)
REVERT: A  107 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8017 (pt0)
REVERT: B   53 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8772 (tm-30)
REVERT: B   91 LYS cc_start: 0.8893 (tttt) cc_final: 0.8332 (tptp)
REVERT: C   36 LYS cc_start: 0.9228 (mptt) cc_final: 0.8976 (mmtm)
REVERT: C   56 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8772 (tm-30)
REVERT: C   71 ARG cc_start: 0.9030 (ttm110) cc_final: 0.8664 (ttp80)
REVERT: C  104 GLN cc_start: 0.8786 (mp10) cc_final: 0.8163 (mp10)
REVERT: D   34 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8412 (mptt)
REVERT: D   68 ASP cc_start: 0.8592 (t70) cc_final: 0.8194 (t0)
REVERT: D   71 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: E   53 LYS cc_start: 0.9313 (tppp) cc_final: 0.8985 (tppt)
REVERT: E   73 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8200 (tm-30)
REVERT: F   24 ASP cc_start: 0.8752 (t0) cc_final: 0.8496 (t0)
REVERT: F   64 ASN cc_start: 0.9140 (t0) cc_final: 0.8242 (t0)
REVERT: F   93 GLN cc_start: 0.8070 (mt0) cc_final: 0.6998 (mt0)
REVERT: G   24 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8113 (mp10)
REVERT: H   42 TYR cc_start: 0.7882 (t80) cc_final: 0.7677 (t80)
REVERT: H   68 ASP cc_start: 0.9295 (t0) cc_final: 0.8828 (t0)
REVERT: H   76 GLU cc_start: 0.8534 (tp30) cc_final: 0.8230 (tp30)
REVERT: H   83 TYR cc_start: 0.8807 (m-80) cc_final: 0.8505 (m-80)
REVERT: H   93 GLU cc_start: 0.8903 (mp0) cc_final: 0.8531 (mp0)
  outliers start: 28
  outliers final: 24
  residues processed: 195
  average time/residue: 0.2524
  time to fit residues: 68.6556
Evaluate side-chains
  200 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   57 VAL
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   62 ILE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain 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 70 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.087227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.060353 restraints weight = 40689.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.062322 restraints weight = 20388.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.063564 restraints weight = 13743.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12880  Z= 0.156
  Angle     :  0.573   6.710  18637  Z= 0.339
  Chirality :  0.033   0.156   2114
  Planarity :  0.003   0.043   1347
  Dihedral  : 30.523 167.931   4019
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 26.96 %
    Favored  : 70.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.30), residues: 753
  helix:  1.72 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.05 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  47 
 HIS   0.002   0.000   HIS E 115 
 PHE   0.009   0.001   PHE A  78 
 TYR   0.048   0.002   TYR D  83 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05887 (  710)
  hydrogen bonds       : angle       2.59079 ( 1730)
  covalent geometry    : bond        0.00341 (12880)
  covalent geometry    : angle       0.57281 (18637)

*********************** 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
  211 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8219 (pp30) cc_final: 0.7896 (pm20)
REVERT: A  107 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7814 (pt0)
REVERT: B   53 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8616 (tm-30)
REVERT: B   91 LYS cc_start: 0.8816 (tttt) cc_final: 0.8302 (tptp)
REVERT: C   36 LYS cc_start: 0.9211 (mptt) cc_final: 0.8969 (mmtm)
REVERT: C   56 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8471 (tm-30)
REVERT: C   57 TYR cc_start: 0.9050 (t80) cc_final: 0.8749 (t80)
REVERT: C   71 ARG cc_start: 0.9051 (ttm110) cc_final: 0.8684 (ttp80)
REVERT: C  104 GLN cc_start: 0.8716 (mp10) cc_final: 0.8057 (mp10)
REVERT: D   34 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8417 (mptt)
REVERT: D   68 ASP cc_start: 0.8452 (t70) cc_final: 0.8043 (t0)
REVERT: D   71 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: E   53 LYS cc_start: 0.9270 (tppp) cc_final: 0.8947 (tppt)
REVERT: E   73 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: F   24 ASP cc_start: 0.8746 (t0) cc_final: 0.8489 (t0)
REVERT: F   64 ASN cc_start: 0.9230 (t0) cc_final: 0.8274 (t0)
REVERT: F   88 TYR cc_start: 0.8482 (m-10) cc_final: 0.7719 (m-10)
REVERT: F   93 GLN cc_start: 0.8002 (mt0) cc_final: 0.7011 (mt0)
REVERT: G   24 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7988 (mp10)
REVERT: G   81 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7830 (tpt170)
REVERT: G  111 ILE cc_start: 0.6727 (OUTLIER) cc_final: 0.6310 (pt)
REVERT: H   68 ASP cc_start: 0.9196 (t0) cc_final: 0.8758 (t0)
REVERT: H   76 GLU cc_start: 0.8470 (tp30) cc_final: 0.8074 (tp30)
REVERT: H   83 TYR cc_start: 0.8585 (m-80) cc_final: 0.8253 (m-80)
REVERT: H   93 GLU cc_start: 0.8846 (mp0) cc_final: 0.8448 (mp0)
  outliers start: 16
  outliers final: 12
  residues processed: 201
  average time/residue: 0.2532
  time to fit residues: 70.9718
Evaluate side-chains
  193 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 179
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  107 GLU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   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 4 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 87 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 27 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.085704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.058454 restraints weight = 40537.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.060268 restraints weight = 20760.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.061445 restraints weight = 14274.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  12880  Z= 0.205
  Angle     :  0.602   7.437  18637  Z= 0.353
  Chirality :  0.034   0.162   2114
  Planarity :  0.004   0.042   1347
  Dihedral  : 30.550 163.478   4019
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 28.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.30), residues: 753
  helix:  1.79 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.05 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP V 530 
 HIS   0.017   0.001   HIS D  82 
 PHE   0.008   0.001   PHE A  78 
 TYR   0.068   0.003   TYR D  83 
 ARG   0.004   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06015 (  710)
  hydrogen bonds       : angle       2.78089 ( 1730)
  covalent geometry    : bond        0.00460 (12880)
  covalent geometry    : angle       0.60199 (18637)

*********************** 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
  200 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 179
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8229 (pp30) cc_final: 0.7854 (pm20)
REVERT: B   53 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8687 (tm-30)
REVERT: B   91 LYS cc_start: 0.8835 (tttt) cc_final: 0.8322 (tptp)
REVERT: B   93 GLN cc_start: 0.8456 (tt0) cc_final: 0.8232 (tt0)
REVERT: C   36 LYS cc_start: 0.9210 (mptt) cc_final: 0.8953 (mmtm)
REVERT: C   56 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8740 (tm-30)
REVERT: C   71 ARG cc_start: 0.9044 (ttm110) cc_final: 0.8674 (ttp80)
REVERT: C  104 GLN cc_start: 0.8778 (mp10) cc_final: 0.8136 (mp10)
REVERT: D   34 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8409 (mptt)
REVERT: D   68 ASP cc_start: 0.8527 (t70) cc_final: 0.8129 (t0)
REVERT: D   71 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: E   53 LYS cc_start: 0.9286 (tppp) cc_final: 0.8980 (tppt)
REVERT: E   73 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: F   24 ASP cc_start: 0.8757 (t0) cc_final: 0.8499 (t0)
REVERT: F   64 ASN cc_start: 0.9157 (t0) cc_final: 0.8231 (t0)
REVERT: F   93 GLN cc_start: 0.8052 (mt0) cc_final: 0.7045 (mt0)
REVERT: G   24 GLN cc_start: 0.8595 (mm-40) cc_final: 0.7971 (mp10)
REVERT: G  111 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6348 (pt)
REVERT: H   68 ASP cc_start: 0.9255 (t0) cc_final: 0.8777 (t0)
REVERT: H   76 GLU cc_start: 0.8565 (tp30) cc_final: 0.8206 (tp30)
REVERT: H   93 GLU cc_start: 0.8854 (mp0) cc_final: 0.8505 (mp0)
  outliers start: 21
  outliers final: 17
  residues processed: 190
  average time/residue: 0.2516
  time to fit residues: 66.9492
Evaluate side-chains
  192 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   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 69 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 98 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 67 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.086923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.060744 restraints weight = 40927.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.062701 restraints weight = 20021.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.063941 restraints weight = 13309.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12880  Z= 0.158
  Angle     :  0.590   8.195  18637  Z= 0.346
  Chirality :  0.033   0.177   2114
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.410 159.869   4019
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 29.62 %
    Favored  : 67.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.30), residues: 753
  helix:  1.84 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.04 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  47 
 HIS   0.018   0.001   HIS D  82 
 PHE   0.028   0.001   PHE A  84 
 TYR   0.088   0.003   TYR D  83 
 ARG   0.003   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05869 (  710)
  hydrogen bonds       : angle       2.62705 ( 1730)
  covalent geometry    : bond        0.00348 (12880)
  covalent geometry    : angle       0.59019 (18637)

*********************** 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
  199 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8252 (pp30) cc_final: 0.7929 (pm20)
REVERT: B   53 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8550 (tm-30)
REVERT: B   91 LYS cc_start: 0.8751 (tttt) cc_final: 0.8267 (tptp)
REVERT: B   93 GLN cc_start: 0.8355 (tt0) cc_final: 0.8140 (tt0)
REVERT: C   36 LYS cc_start: 0.9223 (mptt) cc_final: 0.8959 (mmtm)
REVERT: C   39 TYR cc_start: 0.8937 (m-80) cc_final: 0.8701 (m-80)
REVERT: C   56 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8535 (tm-30)
REVERT: C   57 TYR cc_start: 0.9049 (t80) cc_final: 0.8744 (t80)
REVERT: C   71 ARG cc_start: 0.9021 (ttm110) cc_final: 0.8658 (ttp80)
REVERT: C  104 GLN cc_start: 0.8727 (mp10) cc_final: 0.8105 (mp10)
REVERT: D   34 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8418 (mptt)
REVERT: D   47 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8814 (tt0)
REVERT: D   71 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: E   53 LYS cc_start: 0.9273 (tppp) cc_final: 0.8983 (tppt)
REVERT: F   24 ASP cc_start: 0.8725 (t0) cc_final: 0.8496 (t0)
REVERT: F   64 ASN cc_start: 0.9197 (t0) cc_final: 0.8252 (t0)
REVERT: F   93 GLN cc_start: 0.8019 (mt0) cc_final: 0.7086 (mt0)
REVERT: G   24 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8010 (mp10)
REVERT: G  111 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6293 (pt)
REVERT: H   68 ASP cc_start: 0.9202 (t0) cc_final: 0.8727 (t0)
REVERT: H   76 GLU cc_start: 0.8491 (tp30) cc_final: 0.8102 (tp30)
REVERT: H   93 GLU cc_start: 0.8843 (mp0) cc_final: 0.8491 (mp0)
  outliers start: 17
  outliers final: 14
  residues processed: 189
  average time/residue: 0.2396
  time to fit residues: 64.0321
Evaluate side-chains
  191 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   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 5 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 95 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.085391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.058828 restraints weight = 41121.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.060693 restraints weight = 20463.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.061883 restraints weight = 13804.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12880  Z= 0.200
  Angle     :  0.613   9.857  18637  Z= 0.357
  Chirality :  0.034   0.180   2114
  Planarity :  0.004   0.044   1347
  Dihedral  : 30.456 160.894   4019
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 30.25 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.30), residues: 753
  helix:  1.81 (0.23), residues: 517
  sheet:  None (None), residues: 0
  loop : -1.06 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP V 530 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.020   0.001   PHE A  84 
 TYR   0.084   0.003   TYR D  83 
 ARG   0.004   0.000   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06014 (  710)
  hydrogen bonds       : angle       2.78119 ( 1730)
  covalent geometry    : bond        0.00447 (12880)
  covalent geometry    : angle       0.61345 (18637)

*********************** 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
  196 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8253 (pp30) cc_final: 0.7884 (pm20)
REVERT: A   96 GLU cc_start: 0.8727 (tp30) cc_final: 0.8467 (mm-30)
REVERT: B   53 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8655 (tm-30)
REVERT: B   91 LYS cc_start: 0.8821 (tttt) cc_final: 0.8339 (tptp)
REVERT: B   93 GLN cc_start: 0.8446 (tt0) cc_final: 0.8194 (tt0)
REVERT: C   36 LYS cc_start: 0.9235 (mptt) cc_final: 0.8961 (mmtm)
REVERT: C   56 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8729 (tm-30)
REVERT: C   57 TYR cc_start: 0.9160 (t80) cc_final: 0.8890 (t80)
REVERT: C   71 ARG cc_start: 0.9033 (ttm110) cc_final: 0.8693 (ttp80)
REVERT: C  104 GLN cc_start: 0.8782 (mp10) cc_final: 0.8172 (mp10)
REVERT: D   34 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8446 (mptt)
REVERT: D   68 ASP cc_start: 0.8495 (t70) cc_final: 0.8103 (t0)
REVERT: D   71 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: E   53 LYS cc_start: 0.9301 (tppp) cc_final: 0.9014 (tppt)
REVERT: F   24 ASP cc_start: 0.8730 (t0) cc_final: 0.8477 (t0)
REVERT: F   64 ASN cc_start: 0.9129 (t0) cc_final: 0.8184 (t0)
REVERT: F   93 GLN cc_start: 0.8054 (mt0) cc_final: 0.7228 (mt0)
REVERT: G   24 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8015 (mp10)
REVERT: G   36 LYS cc_start: 0.9086 (tppp) cc_final: 0.8880 (tppp)
REVERT: G  111 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6436 (pt)
REVERT: H   68 ASP cc_start: 0.9239 (t0) cc_final: 0.8787 (t0)
REVERT: H   76 GLU cc_start: 0.8552 (tp30) cc_final: 0.8224 (tp30)
REVERT: H   93 GLU cc_start: 0.8848 (mp0) cc_final: 0.8542 (mp0)
  outliers start: 16
  outliers final: 14
  residues processed: 186
  average time/residue: 0.2536
  time to fit residues: 66.7404
Evaluate side-chains
  191 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   90 THR
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 45 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 54 optimal weight:    0.3980
   chunk 71 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 93 optimal weight:    8.9990
   chunk 100 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.086235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.059949 restraints weight = 40484.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.061841 restraints weight = 20110.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.063037 restraints weight = 13528.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12880  Z= 0.174
  Angle     :  0.607   8.598  18637  Z= 0.354
  Chirality :  0.033   0.172   2114
  Planarity :  0.004   0.045   1347
  Dihedral  : 30.404 163.520   4019
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 30.56 %
    Favored  : 66.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.30), residues: 753
  helix:  1.86 (0.23), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.00 (0.36), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  47 
 HIS   0.017   0.001   HIS D  82 
 PHE   0.015   0.001   PHE A  84 
 TYR   0.080   0.003   TYR D  83 
 ARG   0.002   0.000   ARG B  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05876 (  710)
  hydrogen bonds       : angle       2.74340 ( 1730)
  covalent geometry    : bond        0.00387 (12880)
  covalent geometry    : angle       0.60717 (18637)

********************** 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
  201 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 183
  time to evaluate  : 1.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 GLN cc_start: 0.8205 (pp30) cc_final: 0.7890 (pm20)
REVERT: A   96 GLU cc_start: 0.8711 (tp30) cc_final: 0.8433 (mm-30)
REVERT: B   53 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8606 (tm-30)
REVERT: B   91 LYS cc_start: 0.8710 (tttt) cc_final: 0.8303 (tptp)
REVERT: B   93 GLN cc_start: 0.8408 (tt0) cc_final: 0.8157 (tt0)
REVERT: C   36 LYS cc_start: 0.9191 (mptt) cc_final: 0.8914 (mmtm)
REVERT: C   56 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8523 (tm-30)
REVERT: C   57 TYR cc_start: 0.9106 (t80) cc_final: 0.8798 (t80)
REVERT: C   63 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9269 (mm)
REVERT: C   71 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8671 (ttp80)
REVERT: C  104 GLN cc_start: 0.8774 (mp10) cc_final: 0.8177 (mp10)
REVERT: D   34 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8454 (mptt)
REVERT: D   47 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8810 (tt0)
REVERT: D   68 ASP cc_start: 0.8458 (t70) cc_final: 0.8069 (t0)
REVERT: D   71 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8358 (tm-30)
REVERT: D   83 TYR cc_start: 0.6210 (m-80) cc_final: 0.5173 (m-80)
REVERT: E   53 LYS cc_start: 0.9297 (tppp) cc_final: 0.9017 (tppt)
REVERT: F   24 ASP cc_start: 0.8756 (t0) cc_final: 0.8528 (t0)
REVERT: F   64 ASN cc_start: 0.9161 (t0) cc_final: 0.8201 (t0)
REVERT: F   93 GLN cc_start: 0.8009 (mt0) cc_final: 0.7062 (mt0)
REVERT: G   24 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8035 (mp10)
REVERT: G  111 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6404 (pt)
REVERT: H   68 ASP cc_start: 0.9211 (t0) cc_final: 0.8751 (t0)
REVERT: H   76 GLU cc_start: 0.8563 (tp30) cc_final: 0.8179 (tp30)
REVERT: H   93 GLU cc_start: 0.8861 (mp0) cc_final: 0.8539 (mp0)
  outliers start: 18
  outliers final: 15
  residues processed: 190
  average time/residue: 0.3513
  time to fit residues: 96.0564
Evaluate side-chains
  196 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  127 GLN
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   82 HIS
Chi-restraints excluded: chain E residue   82 VAL
Chi-restraints excluded: chain E residue  135 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   90 THR
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 69 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 14 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 56 optimal weight:    7.9990
   chunk 90 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 88 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.087350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.061280 restraints weight = 40904.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.063169 restraints weight = 20283.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.064400 restraints weight = 13592.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12880  Z= 0.161
  Angle     :  0.597   7.634  18637  Z= 0.349
  Chirality :  0.033   0.181   2114
  Planarity :  0.004   0.045   1347
  Dihedral  : 30.364 167.279   4019
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 30.72 %
    Favored  : 66.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.30), residues: 753
  helix:  1.97 (0.23), residues: 514
  sheet:  None (None), residues: 0
  loop : -0.98 (0.36), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  47 
 HIS   0.017   0.001   HIS D  82 
 PHE   0.011   0.001   PHE A  84 
 TYR   0.060   0.003   TYR D  83 
 ARG   0.003   0.000   ARG D  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05797 (  710)
  hydrogen bonds       : angle       2.69421 ( 1730)
  covalent geometry    : bond        0.00355 (12880)
  covalent geometry    : angle       0.59685 (18637)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4130.68 seconds
wall clock time: 74 minutes 10.31 seconds (4450.31 seconds total)