Starting phenix.real_space_refine
on Sun Aug 24 02:46:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ynl_39426/08_2025/8ynl_39426.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ynl_39426/08_2025/8ynl_39426.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ynl_39426/08_2025/8ynl_39426.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ynl_39426/08_2025/8ynl_39426.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ynl_39426/08_2025/8ynl_39426.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ynl_39426/08_2025/8ynl_39426.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4446 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      74      5.16       5
     C    8243      2.51       5
     N    2226      2.21       5
     O    2434      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12977
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1510
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 3, 'TRANS': 178}
    Chain: "B"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1510
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 3, 'TRANS': 178}
    Chain: "C"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1510
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 3, 'TRANS': 178}
    Chain: "H"
      Number of atoms: 1403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1403
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1386
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 4, 'TRANS': 165}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1386
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 4, 'TRANS': 165}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1424
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
    Chain: "G"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1424
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
    Chain: "F"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1424
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
  Time building chain proxies: 3.66, per 1000 atoms: 0.28
  Number of scatterers: 12977
  At special positions: 0
  Unit cell: (104.16, 101.64, 146.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      74     16.00
     O    2434      8.00
     N    2226      7.00
     C    8243      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 620.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3074

  Finding SS restraints...
    Secondary structure from input PDB file:
      107 helices and 0 sheets defined
      76.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 12
    Processing helix  chain 'A' and resid 15 through 26
    Processing helix  chain 'A' and resid 31 through 36
    Processing helix  chain 'A' and resid 40 through 51
      removed outlier: 3.606A  pdb=" N   LEU A  44 " --> pdb=" O   ASP A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 71 through 78
      removed outlier: 4.106A  pdb=" N   LEU A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 92
      removed outlier: 3.585A  pdb=" N   MET A  86 " --> pdb=" O   ARG A  82 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   THR A  92 " --> pdb=" O   ARG A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 111
      removed outlier: 3.552A  pdb=" N   VAL A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU A 111 " --> pdb=" O   GLN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 124
    Processing helix  chain 'A' and resid 129 through 134
      removed outlier: 3.848A  pdb=" N   ASP A 134 " --> pdb=" O   CYS A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 149
    Processing helix  chain 'A' and resid 157 through 168
      removed outlier: 4.124A  pdb=" N   GLN A 166 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ILE A 167 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 182
    Processing helix  chain 'B' and resid 2 through 12
    Processing helix  chain 'B' and resid 15 through 26
    Processing helix  chain 'B' and resid 31 through 36
    Processing helix  chain 'B' and resid 40 through 51
      removed outlier: 3.767A  pdb=" N   LEU B  44 " --> pdb=" O   ASP B  40 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LYS B  51 " --> pdb=" O   ARG B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 69
      removed outlier: 3.617A  pdb=" N   ILE B  69 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 79
      removed outlier: 4.003A  pdb=" N   LEU B  75 " --> pdb=" O   ARG B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'B' and resid 99 through 110
    Processing helix  chain 'B' and resid 113 through 124
    Processing helix  chain 'B' and resid 129 through 134
      removed outlier: 3.828A  pdb=" N   ASP B 134 " --> pdb=" O   CYS B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 149
      removed outlier: 3.578A  pdb=" N   ILE B 142 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 165
    Processing helix  chain 'B' and resid 169 through 182
    Processing helix  chain 'C' and resid 2 through 14
      removed outlier: 3.837A  pdb=" N   GLN C  13 " --> pdb=" O   ASP C   9 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LEU C  14 " --> pdb=" O   ILE C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 26
    Processing helix  chain 'C' and resid 31 through 36
    Processing helix  chain 'C' and resid 40 through 51
      removed outlier: 3.502A  pdb=" N   LEU C  44 " --> pdb=" O   ASP C  40 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS C  51 " --> pdb=" O   ARG C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 71 through 79
      removed outlier: 3.736A  pdb=" N   LEU C  75 " --> pdb=" O   ARG C  71 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU C  79 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 92
    Processing helix  chain 'C' and resid 99 through 111
    Processing helix  chain 'C' and resid 113 through 124
    Processing helix  chain 'C' and resid 130 through 134
    Processing helix  chain 'C' and resid 138 through 149
    Processing helix  chain 'C' and resid 157 through 165
    Processing helix  chain 'C' and resid 169 through 182
    Processing helix  chain 'H' and resid 3 through 12
      removed outlier: 3.880A  pdb=" N   HIS H   7 " --> pdb=" O   ALA H   3 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 14 through 26
    Processing helix  chain 'H' and resid 36 through 47
    Processing helix  chain 'H' and resid 51 through 61
    Processing helix  chain 'H' and resid 64 through 71
    Processing helix  chain 'H' and resid 75 through 86
      removed outlier: 3.551A  pdb=" N   VAL H  79 " --> pdb=" O   ASP H  75 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 91 through 102
    Processing helix  chain 'H' and resid 105 through 117
    Processing helix  chain 'H' and resid 121 through 126
    Processing helix  chain 'H' and resid 130 through 142
    Processing helix  chain 'H' and resid 149 through 159
    Processing helix  chain 'H' and resid 162 through 174
    Processing helix  chain 'I' and resid 2 through 13
      removed outlier: 3.654A  pdb=" N   ILE I   6 " --> pdb=" O   SER I   2 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 14 through 25
    Processing helix  chain 'I' and resid 26 through 30
      removed outlier: 3.867A  pdb=" N   ILE I  30 " --> pdb=" O   ASP I  27 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 36 through 47
    Processing helix  chain 'I' and resid 51 through 61
    Processing helix  chain 'I' and resid 64 through 71
    Processing helix  chain 'I' and resid 75 through 86
    Processing helix  chain 'I' and resid 91 through 102
      removed outlier: 3.609A  pdb=" N   VAL I  95 " --> pdb=" O   SER I  91 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 105 through 117
    Processing helix  chain 'I' and resid 130 through 141
    Processing helix  chain 'I' and resid 149 through 159
    Processing helix  chain 'I' and resid 161 through 176
      removed outlier: 3.859A  pdb=" N   LYS I 165 " --> pdb=" O   ARG I 161 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN I 176 " --> pdb=" O   LYS I 172 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 13
      removed outlier: 3.641A  pdb=" N   ILE J   6 " --> pdb=" O   SER J   2 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 14 through 26
    Processing helix  chain 'J' and resid 36 through 47
    Processing helix  chain 'J' and resid 51 through 62
    Processing helix  chain 'J' and resid 64 through 71
      removed outlier: 3.743A  pdb=" N   LEU J  68 " --> pdb=" O   ARG J  64 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 75 through 86
    Processing helix  chain 'J' and resid 91 through 103
      removed outlier: 3.531A  pdb=" N   VAL J  95 " --> pdb=" O   SER J  91 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP J 103 " --> pdb=" O   GLU J  99 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 107 through 117
    Processing helix  chain 'J' and resid 130 through 141
    Processing helix  chain 'J' and resid 149 through 159
    Processing helix  chain 'J' and resid 161 through 175
      removed outlier: 3.957A  pdb=" N   LYS J 165 " --> pdb=" O   ARG J 161 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 12
      removed outlier: 3.724A  pdb=" N   ILE K   6 " --> pdb=" O   SER K   2 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 14 through 25
      removed outlier: 3.619A  pdb=" N   LYS K  18 " --> pdb=" O   ASP K  14 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLU K  19 " --> pdb=" O   THR K  15 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   MET K  20 " --> pdb=" O   ASP K  16 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 47
    Processing helix  chain 'K' and resid 51 through 62
    Processing helix  chain 'K' and resid 64 through 71
    Processing helix  chain 'K' and resid 75 through 86
      removed outlier: 3.631A  pdb=" N   VAL K  79 " --> pdb=" O   ASP K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 91 through 102
      removed outlier: 3.530A  pdb=" N   VAL K  95 " --> pdb=" O   SER K  91 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 105 through 116
      removed outlier: 3.560A  pdb=" N   VAL K 109 " --> pdb=" O   ASP K 105 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER K 110 " --> pdb=" O   LYS K 106 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   SER K 111 " --> pdb=" O   SER K 107 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 130 through 141
    Processing helix  chain 'K' and resid 149 through 159
    Processing helix  chain 'K' and resid 162 through 175
    Processing helix  chain 'G' and resid 2 through 12
      removed outlier: 3.728A  pdb=" N   ILE G   6 " --> pdb=" O   SER G   2 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 25
      removed outlier: 3.663A  pdb=" N   GLU G  19 " --> pdb=" O   THR G  15 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   MET G  20 " --> pdb=" O   ASP G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 47
    Processing helix  chain 'G' and resid 51 through 62
    Processing helix  chain 'G' and resid 64 through 71
    Processing helix  chain 'G' and resid 75 through 85
    Processing helix  chain 'G' and resid 91 through 103
    Processing helix  chain 'G' and resid 105 through 116
      removed outlier: 4.121A  pdb=" N   SER G 111 " --> pdb=" O   SER G 107 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 130 through 141
    Processing helix  chain 'G' and resid 149 through 159
      removed outlier: 3.516A  pdb=" N   ILE G 159 " --> pdb=" O   CYS G 155 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 162 through 175
      removed outlier: 3.644A  pdb=" N   VAL G 175 " --> pdb=" O   TYR G 171 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 2 through 13
      removed outlier: 3.550A  pdb=" N   LEU F  13 " --> pdb=" O   VAL F   9 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 14 through 25
      removed outlier: 3.591A  pdb=" N   LYS F  18 " --> pdb=" O   ASP F  14 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   GLU F  19 " --> pdb=" O   THR F  15 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   MET F  20 " --> pdb=" O   ASP F  16 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 36 through 47
    Processing helix  chain 'F' and resid 51 through 62
      removed outlier: 3.523A  pdb=" N   VAL F  62 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 64 through 71
    Processing helix  chain 'F' and resid 75 through 86
      removed outlier: 3.524A  pdb=" N   VAL F  79 " --> pdb=" O   ASP F  75 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 104
    Processing helix  chain 'F' and resid 105 through 117
      removed outlier: 3.617A  pdb=" N   SER F 111 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 130 through 141
    Processing helix  chain 'F' and resid 149 through 158
    Processing helix  chain 'F' and resid 161 through 175
      removed outlier: 4.027A  pdb=" N   LYS F 165 " --> pdb=" O   ARG F 161 " (cutoff:3.500A)

    724 hydrogen bonds defined for protein.
    2151 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4343
        1.34 -     1.46: 2271
        1.46 -     1.58: 6368
        1.58 -     1.69: 0
        1.69 -     1.81: 130
  Bond restraints: 13112
  Sorted by residual:
  bond pdb=" CA  THR H 166 "
       pdb=" C   THR H 166 "
    ideal  model  delta    sigma   weight residual
    1.524  1.499  0.025 1.26e-02 6.30e+03 4.00e+00
  bond pdb=" C   THR H 166 "
       pdb=" N   LYS H 167 "
    ideal  model  delta    sigma   weight residual
    1.335  1.323  0.011 1.25e-02 6.40e+03 8.11e-01
  bond pdb=" CA  PRO H  34 "
       pdb=" C   PRO H  34 "
    ideal  model  delta    sigma   weight residual
    1.517  1.511  0.006 6.70e-03 2.23e+04 6.76e-01
  bond pdb=" C   ILE B 151 "
       pdb=" N   LEU B 152 "
    ideal  model  delta    sigma   weight residual
    1.330  1.341 -0.011 1.36e-02 5.41e+03 6.26e-01
  bond pdb=" CB  PRO H  87 "
       pdb=" CG  PRO H  87 "
    ideal  model  delta    sigma   weight residual
    1.492  1.529 -0.037 5.00e-02 4.00e+02 5.41e-01
  ... (remaining 13107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 17121
        1.00 -     1.99: 352
        1.99 -     2.99: 61
        2.99 -     3.98: 24
        3.98 -     4.98: 11
  Bond angle restraints: 17569
  Sorted by residual:
  angle pdb=" N   THR H 166 "
        pdb=" CA  THR H 166 "
        pdb=" C   THR H 166 "
      ideal   model   delta    sigma   weight residual
     111.14  106.35    4.79 1.08e+00 8.57e-01 1.97e+01
  angle pdb=" N   ILE A  69 "
        pdb=" CA  ILE A  69 "
        pdb=" C   ILE A  69 "
      ideal   model   delta    sigma   weight residual
     112.29  108.98    3.31 9.40e-01 1.13e+00 1.24e+01
  angle pdb=" N   VAL J  62 "
        pdb=" CA  VAL J  62 "
        pdb=" C   VAL J  62 "
      ideal   model   delta    sigma   weight residual
     112.98  108.68    4.30 1.25e+00 6.40e-01 1.18e+01
  angle pdb=" CA  THR H 166 "
        pdb=" CB  THR H 166 "
        pdb=" OG1 THR H 166 "
      ideal   model   delta    sigma   weight residual
     109.60  104.62    4.98 1.50e+00 4.44e-01 1.10e+01
  angle pdb=" C   LYS H 165 "
        pdb=" N   THR H 166 "
        pdb=" CA  THR H 166 "
      ideal   model   delta    sigma   weight residual
     120.44  116.90    3.54 1.36e+00 5.41e-01 6.78e+00
  ... (remaining 17564 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 7451
       17.54 -    35.08: 738
       35.08 -    52.62: 107
       52.62 -    70.16: 18
       70.16 -    87.69: 15
  Dihedral angle restraints: 8329
    sinusoidal: 3642
      harmonic: 4687
  Sorted by residual:
  dihedral pdb=" CA  ASP A  73 "
           pdb=" CB  ASP A  73 "
           pdb=" CG  ASP A  73 "
           pdb=" OD1 ASP A  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.67   56.67     1      2.00e+01 2.50e-03 1.08e+01
  dihedral pdb=" CB  GLU B  12 "
           pdb=" CG  GLU B  12 "
           pdb=" CD  GLU B  12 "
           pdb=" OE1 GLU B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.29   85.29     1      3.00e+01 1.11e-03 9.79e+00
  dihedral pdb=" CB  MET G  97 "
           pdb=" CG  MET G  97 "
           pdb=" SD  MET G  97 "
           pdb=" CE  MET G  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.91   59.09     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 8326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1432
       0.028 -    0.056: 414
       0.056 -    0.084: 149
       0.084 -    0.113: 45
       0.113 -    0.141: 10
  Chirality restraints: 2050
  Sorted by residual:
  chirality pdb=" CB  VAL F  62 "
            pdb=" CA  VAL F  62 "
            pdb=" CG1 VAL F  62 "
            pdb=" CG2 VAL F  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CB  VAL A 150 "
            pdb=" CA  VAL A 150 "
            pdb=" CG1 VAL A 150 "
            pdb=" CG2 VAL A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.47e-01
  chirality pdb=" CB  VAL C 150 "
            pdb=" CA  VAL C 150 "
            pdb=" CG1 VAL C 150 "
            pdb=" CG2 VAL C 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 2047 not shown)

  Planarity restraints: 2230
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS H 165 "   -0.007 2.00e-02 2.50e+03   1.33e-02 1.77e+00
        pdb=" C   LYS H 165 "    0.023 2.00e-02 2.50e+03
        pdb=" O   LYS H 165 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   THR H 166 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 145 "    0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO F 146 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO F 146 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO F 146 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA I 145 "    0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO I 146 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO I 146 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO I 146 "    0.015 5.00e-02 4.00e+02
  ... (remaining 2227 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 3144
        2.80 -     3.33: 12718
        3.33 -     3.85: 19691
        3.85 -     4.38: 21996
        4.38 -     4.90: 38279
  Nonbonded interactions: 95828
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU F  17 "
            pdb=" NH2 ARG F  64 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" O   ASP K 163 "
            pdb=" OG1 THR K 166 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OE1 GLU G  17 "
            pdb=" NH2 ARG G  64 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OD1 ASP B  28 "
            pdb=" NH2 ARG B 102 "
     model   vdw
     2.308 3.120
  nonbonded pdb=" O   ASP G 163 "
            pdb=" OG1 THR G 166 "
     model   vdw
     2.320 3.040
  ... (remaining 95823 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 'B'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'F' and (resid 2 through 28 or resid 31 through 121 or resid 128 through  \ 
175))
  selection = (chain 'G' and (resid 2 through 28 or resid 31 through 121 or resid 128 through  \ 
175))
  selection = (chain 'H' and (resid 2 through 121 or resid 128 through 175))
  selection = (chain 'I' and (resid 2 through 28 or resid 31 through 175))
  selection = (chain 'J' and (resid 2 through 28 or resid 31 through 121 or resid 128 through  \ 
175))
  selection = (chain 'K' and (resid 2 through 28 or resid 31 through 121 or resid 128 through  \ 
175))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     13.510
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
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      :  0.002   0.037  13112  Z= 0.083
  Angle     :  0.390   4.980  17569  Z= 0.221
  Chirality :  0.033   0.141   2050
  Planarity :  0.002   0.028   2230
  Dihedral  : 13.834  87.694   5255
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.22), residues: 1559
  helix:  1.94 (0.16), residues: 1171
  sheet:  None (None), residues: 0
  loop : -0.96 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG K  64 
 TYR   0.010   0.001   TYR C 101 
 PHE   0.011   0.001   PHE B   3 
 HIS   0.002   0.000   HIS F 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00170 (13112)
  covalent geometry    : angle       0.38982 (17569)
  hydrogen bonds       : bond        0.15677 (  724)
  hydrogen bonds       : angle       4.35926 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  367 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 367
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.8322 (t80) cc_final: 0.8037 (t80)
REVERT: B  172 LEU cc_start: 0.9114 (mp) cc_final: 0.8893 (mm)
REVERT: C    1 MET cc_start: 0.6163 (ptt) cc_final: 0.5920 (ttt)
REVERT: C   29 TYR cc_start: 0.8558 (m-80) cc_final: 0.8303 (m-80)
REVERT: C   34 LYS cc_start: 0.8550 (mmtm) cc_final: 0.8289 (mttt)
REVERT: C   46 GLN cc_start: 0.8480 (mt0) cc_final: 0.8268 (mt0)
REVERT: C   95 ARG cc_start: 0.7532 (mmt90) cc_final: 0.6868 (tpp80)
REVERT: C  101 TYR cc_start: 0.7802 (t80) cc_final: 0.7541 (t80)
REVERT: C  124 LEU cc_start: 0.8208 (mt) cc_final: 0.7681 (pp)
REVERT: C  163 VAL cc_start: 0.9215 (t) cc_final: 0.8761 (p)
REVERT: C  181 PHE cc_start: 0.7862 (m-10) cc_final: 0.7308 (m-80)
REVERT: I    6 ILE cc_start: 0.8891 (pt) cc_final: 0.8568 (mt)
REVERT: I   86 ASN cc_start: 0.8545 (m-40) cc_final: 0.8070 (m110)
REVERT: J   93 TYR cc_start: 0.8598 (t80) cc_final: 0.8297 (t80)
REVERT: J   97 MET cc_start: 0.8806 (mmt) cc_final: 0.8468 (mmt)
REVERT: K   74 MET cc_start: 0.7815 (mtp) cc_final: 0.7515 (ttm)
REVERT: G    1 MET cc_start: 0.6529 (ttp) cc_final: 0.5969 (mpp)
REVERT: G  133 ASP cc_start: 0.8192 (t0) cc_final: 0.7946 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 367
  average time/residue: 0.1249
  time to fit residues: 65.5615
Evaluate side-chains
  200 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0770
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    0.0570
   chunk 103 optimal weight:    0.0050
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.0980
   chunk 91 optimal weight:    5.9990
   chunk 149 optimal weight:    0.3980
   overall best weight:    0.1270

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN
B 176 ASN
H  88 HIS
I  86 ASN
I 148 GLN
F 142 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.126046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.104174 restraints weight = 29016.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.107212 restraints weight = 14053.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.109262 restraints weight = 8676.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.110623 restraints weight = 6230.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.111509 restraints weight = 4982.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13112  Z= 0.110
  Angle     :  0.526  11.998  17569  Z= 0.272
  Chirality :  0.036   0.196   2050
  Planarity :  0.003   0.042   2230
  Dihedral  :  3.270  12.808   1731
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.59 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.22), residues: 1559
  helix:  1.66 (0.16), residues: 1199
  sheet:  None (None), residues: 0
  loop : -0.67 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG J  85 
 TYR   0.007   0.001   TYR C 101 
 PHE   0.017   0.001   PHE A 120 
 HIS   0.003   0.001   HIS F   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (13112)
  covalent geometry    : angle       0.52591 (17569)
  hydrogen bonds       : bond        0.03423 (  724)
  hydrogen bonds       : angle       3.67012 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 231
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 ARG cc_start: 0.7272 (mmt90) cc_final: 0.6995 (mmt90)
REVERT: C  124 LEU cc_start: 0.7988 (mt) cc_final: 0.7734 (pp)
REVERT: C  163 VAL cc_start: 0.9286 (t) cc_final: 0.9056 (p)
REVERT: H   44 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8727 (mm)
REVERT: H   82 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.8047 (m-70)
REVERT: J    1 MET cc_start: 0.6876 (ttm) cc_final: 0.6605 (ttp)
REVERT: J   11 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7105 (mp0)
REVERT: J   93 TYR cc_start: 0.8426 (t80) cc_final: 0.8113 (t80)
REVERT: J   97 MET cc_start: 0.8858 (mmt) cc_final: 0.8524 (mmt)
REVERT: G   75 ASP cc_start: 0.7491 (p0) cc_final: 0.7156 (p0)
REVERT: G  116 MET cc_start: 0.8574 (mmm) cc_final: 0.8252 (mmm)
REVERT: G  133 ASP cc_start: 0.8019 (t0) cc_final: 0.7817 (t0)
REVERT: F   17 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7931 (mt-10)
  outliers start: 26
  outliers final: 13
  residues processed: 243
  average time/residue: 0.1166
  time to fit residues: 41.7951
Evaluate side-chains
  210 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain H residue   44 LEU
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue  125 ILE
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain I residue  120 MET
Chi-restraints excluded: chain J residue   11 GLU
Chi-restraints excluded: chain J residue   83 LEU
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain F residue  142 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 83 optimal weight:    0.0570
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.0104

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  88 HIS
I  82 HIS
** K 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   8 GLN
F  36 ASN
F  82 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.123532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.101179 restraints weight = 29507.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.104220 restraints weight = 14090.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.106264 restraints weight = 8647.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.107618 restraints weight = 6219.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.108536 restraints weight = 4983.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13112  Z= 0.113
  Angle     :  0.496   7.742  17569  Z= 0.260
  Chirality :  0.037   0.233   2050
  Planarity :  0.003   0.032   2230
  Dihedral  :  3.286  12.438   1731
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.22 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.22), residues: 1559
  helix:  1.65 (0.16), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.69 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG J  85 
 TYR   0.014   0.001   TYR C 101 
 PHE   0.009   0.001   PHE B 120 
 HIS   0.003   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (13112)
  covalent geometry    : angle       0.49637 (17569)
  hydrogen bonds       : bond        0.03265 (  724)
  hydrogen bonds       : angle       3.65932 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 207
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8424 (mm-40)
REVERT: B  146 MET cc_start: 0.8677 (mmm) cc_final: 0.8395 (mtt)
REVERT: C   95 ARG cc_start: 0.7361 (mmt90) cc_final: 0.6985 (mmt90)
REVERT: C  163 VAL cc_start: 0.9269 (t) cc_final: 0.8957 (p)
REVERT: H   82 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.8090 (m-70)
REVERT: J    1 MET cc_start: 0.6889 (ttm) cc_final: 0.6662 (ttp)
REVERT: J   93 TYR cc_start: 0.8535 (t80) cc_final: 0.8136 (t80)
REVERT: J   97 MET cc_start: 0.8817 (mmt) cc_final: 0.8509 (mmt)
REVERT: K   31 ASP cc_start: 0.6915 (p0) cc_final: 0.6686 (t0)
REVERT: G   11 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7519 (mt-10)
REVERT: G  116 MET cc_start: 0.8606 (mmm) cc_final: 0.8120 (mmm)
REVERT: F   17 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7978 (mt-10)
REVERT: F  116 MET cc_start: 0.8153 (mmm) cc_final: 0.7938 (mmt)
  outliers start: 24
  outliers final: 15
  residues processed: 220
  average time/residue: 0.1021
  time to fit residues: 33.8744
Evaluate side-chains
  196 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  181 PHE
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain K residue   39 ASP
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  130 SER
Chi-restraints excluded: chain G residue  112 LEU
Chi-restraints excluded: chain F residue   15 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 147 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 155 optimal weight:    3.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 176 ASN
H  88 HIS
J  82 HIS
G   8 GLN
F  82 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.097290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.073882 restraints weight = 33651.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.076636 restraints weight = 18448.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.078469 restraints weight = 12518.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.079696 restraints weight = 9659.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.080501 restraints weight = 8130.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13112  Z= 0.148
  Angle     :  0.536  10.550  17569  Z= 0.273
  Chirality :  0.037   0.178   2050
  Planarity :  0.003   0.054   2230
  Dihedral  :  3.428  13.606   1731
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 14.18 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1559
  helix:  1.62 (0.16), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.68 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 114 
 TYR   0.010   0.001   TYR B 106 
 PHE   0.012   0.001   PHE A 181 
 HIS   0.008   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (13112)
  covalent geometry    : angle       0.53606 (17569)
  hydrogen bonds       : bond        0.03445 (  724)
  hydrogen bonds       : angle       3.80187 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 194
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8062 (tm-30)
REVERT: A   46 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8486 (mm-40)
REVERT: C   95 ARG cc_start: 0.7462 (mmt90) cc_final: 0.6977 (mmt90)
REVERT: H    8 GLN cc_start: 0.8774 (pt0) cc_final: 0.8555 (tm-30)
REVERT: H   82 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8077 (m-70)
REVERT: J    1 MET cc_start: 0.7022 (ttm) cc_final: 0.6786 (ttp)
REVERT: J   83 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8144 (mt)
REVERT: J   93 TYR cc_start: 0.8691 (t80) cc_final: 0.8210 (t80)
REVERT: K  116 MET cc_start: 0.8219 (mtm) cc_final: 0.7800 (mtm)
REVERT: G  116 MET cc_start: 0.8710 (mmm) cc_final: 0.8400 (mmp)
REVERT: F   64 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7160 (tpp-160)
REVERT: F  116 MET cc_start: 0.8004 (mmm) cc_final: 0.7786 (mmt)
  outliers start: 39
  outliers final: 24
  residues processed: 216
  average time/residue: 0.1019
  time to fit residues: 33.3115
Evaluate side-chains
  203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue    6 ILE
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain J residue   83 LEU
Chi-restraints excluded: chain J residue   84 LEU
Chi-restraints excluded: chain J residue  173 GLN
Chi-restraints excluded: chain K residue    9 VAL
Chi-restraints excluded: chain K residue   39 ASP
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  130 SER
Chi-restraints excluded: chain K residue  175 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue  112 LEU
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain F residue   15 THR
Chi-restraints excluded: chain F residue   64 ARG
Chi-restraints excluded: chain F residue  166 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 145 optimal weight:    3.9990
   chunk 102 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 149 optimal weight:    0.5980
   chunk 99 optimal weight:    3.9990
   chunk 153 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 133 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  88 HIS
G   8 GLN
** F  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.099359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.076296 restraints weight = 33987.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.079223 restraints weight = 17960.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.081143 restraints weight = 11971.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.082373 restraints weight = 9172.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.083219 restraints weight = 7695.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13112  Z= 0.130
  Angle     :  0.516   9.702  17569  Z= 0.264
  Chirality :  0.036   0.153   2050
  Planarity :  0.002   0.030   2230
  Dihedral  :  3.438  15.453   1731
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.94 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.22), residues: 1559
  helix:  1.57 (0.16), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.66 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J  85 
 TYR   0.009   0.001   TYR B 106 
 PHE   0.009   0.001   PHE B 120 
 HIS   0.009   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (13112)
  covalent geometry    : angle       0.51555 (17569)
  hydrogen bonds       : bond        0.03149 (  724)
  hydrogen bonds       : angle       3.74809 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8059 (tm-30)
REVERT: A   46 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8498 (mm-40)
REVERT: A  134 ASP cc_start: 0.8827 (t70) cc_final: 0.8583 (t0)
REVERT: C   95 ARG cc_start: 0.7461 (mmt90) cc_final: 0.7000 (mmt90)
REVERT: H   82 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.8079 (m-70)
REVERT: J    1 MET cc_start: 0.6980 (ttm) cc_final: 0.6755 (ttp)
REVERT: J   97 MET cc_start: 0.8754 (mmt) cc_final: 0.8506 (mmt)
REVERT: K  116 MET cc_start: 0.8036 (mtm) cc_final: 0.7591 (mtm)
REVERT: F   97 MET cc_start: 0.8478 (mmm) cc_final: 0.8023 (mmm)
  outliers start: 29
  outliers final: 21
  residues processed: 209
  average time/residue: 0.0993
  time to fit residues: 31.6022
Evaluate side-chains
  192 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue    6 ILE
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain J residue  173 GLN
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  130 SER
Chi-restraints excluded: chain K residue  175 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue  112 LEU
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain F residue   15 THR
Chi-restraints excluded: chain F residue  166 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 120 optimal weight:    0.0060
   chunk 132 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 115 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
H  88 HIS
** F  82 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 = 0.3642 r_free = 0.3642 target = 0.099986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.077122 restraints weight = 33455.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.080004 restraints weight = 17799.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.081911 restraints weight = 11917.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.083174 restraints weight = 9129.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.083889 restraints weight = 7657.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13112  Z= 0.100
  Angle     :  0.509  10.874  17569  Z= 0.261
  Chirality :  0.036   0.144   2050
  Planarity :  0.003   0.067   2230
  Dihedral  :  3.434  16.234   1731
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 16.61 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.22), residues: 1559
  helix:  1.60 (0.16), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.66 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 114 
 TYR   0.011   0.001   TYR G  93 
 PHE   0.015   0.001   PHE C 143 
 HIS   0.010   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (13112)
  covalent geometry    : angle       0.50917 (17569)
  hydrogen bonds       : bond        0.02785 (  724)
  hydrogen bonds       : angle       3.56256 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: A   46 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8444 (mm-40)
REVERT: C   95 ARG cc_start: 0.7464 (mmt90) cc_final: 0.6976 (mmt90)
REVERT: H   82 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.8084 (m-70)
REVERT: J    1 MET cc_start: 0.6940 (ttm) cc_final: 0.6725 (ttp)
REVERT: J   93 TYR cc_start: 0.8458 (t80) cc_final: 0.7996 (t80)
REVERT: K  116 MET cc_start: 0.7990 (mtm) cc_final: 0.7601 (mtm)
REVERT: G    1 MET cc_start: 0.5727 (mmt) cc_final: 0.5497 (mmt)
REVERT: G   93 TYR cc_start: 0.8113 (t80) cc_final: 0.7821 (t80)
REVERT: G   97 MET cc_start: 0.9178 (mmt) cc_final: 0.8728 (mpp)
REVERT: F   97 MET cc_start: 0.8415 (mmm) cc_final: 0.8026 (mmm)
  outliers start: 21
  outliers final: 18
  residues processed: 197
  average time/residue: 0.0953
  time to fit residues: 28.2751
Evaluate side-chains
  189 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 170
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  141 ASP
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue    4 GLU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain J residue  173 GLN
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  130 SER
Chi-restraints excluded: chain K residue  175 VAL
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue  112 LEU
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 63 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 142 optimal weight:   30.0000
   chunk 24 optimal weight:    1.9990
   chunk 141 optimal weight:    3.9990
   chunk 150 optimal weight:    0.9980
   chunk 83 optimal weight:    4.9990
   chunk 132 optimal weight:    0.0870
   chunk 108 optimal weight:    1.9990
   chunk 111 optimal weight:    2.9990
   chunk 126 optimal weight:    9.9990
   overall best weight:    1.2162

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

Flipped N/Q/H residues before XYZ refinement:
C  35 GLN
H  88 HIS
** G   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  86 ASN
F  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.105865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.083087 restraints weight = 34045.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.086289 restraints weight = 17220.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.088372 restraints weight = 11181.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.089694 restraints weight = 8432.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.090589 restraints weight = 7016.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13112  Z= 0.118
  Angle     :  0.508   7.945  17569  Z= 0.262
  Chirality :  0.036   0.152   2050
  Planarity :  0.002   0.030   2230
  Dihedral  :  3.398  15.436   1731
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.02 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.22), residues: 1559
  helix:  1.59 (0.16), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.63 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  64 
 TYR   0.010   0.001   TYR K  93 
 PHE   0.009   0.001   PHE C 143 
 HIS   0.009   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13112)
  covalent geometry    : angle       0.50797 (17569)
  hydrogen bonds       : bond        0.02910 (  724)
  hydrogen bonds       : angle       3.61414 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 177
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8473 (mm-40)
REVERT: A  134 ASP cc_start: 0.9005 (t70) cc_final: 0.8760 (t70)
REVERT: C   95 ARG cc_start: 0.7491 (mmt90) cc_final: 0.6991 (mmt90)
REVERT: H    8 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7956 (pp30)
REVERT: H   82 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.8096 (m-70)
REVERT: J    1 MET cc_start: 0.6984 (ttm) cc_final: 0.6769 (ttp)
REVERT: J   83 LEU cc_start: 0.8571 (tp) cc_final: 0.8183 (pp)
REVERT: K  116 MET cc_start: 0.7956 (mtm) cc_final: 0.7617 (mtm)
REVERT: G    1 MET cc_start: 0.5775 (mmt) cc_final: 0.5442 (mmt)
REVERT: G   93 TYR cc_start: 0.8122 (t80) cc_final: 0.7887 (t80)
REVERT: G   97 MET cc_start: 0.9162 (mmt) cc_final: 0.8684 (mpp)
  outliers start: 26
  outliers final: 22
  residues processed: 196
  average time/residue: 0.0908
  time to fit residues: 27.4486
Evaluate side-chains
  194 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue    4 GLU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain J residue  173 GLN
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  130 SER
Chi-restraints excluded: chain K residue  175 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue  112 LEU
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain F residue   15 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 89 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 147 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 150 optimal weight:    3.9990
   chunk 131 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0060
   overall best weight:    1.5602

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

Flipped N/Q/H residues before XYZ refinement:
C  35 GLN
H  88 HIS
F  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.101890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.078769 restraints weight = 33770.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.081757 restraints weight = 17813.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.083750 restraints weight = 11836.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.085041 restraints weight = 9041.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.085879 restraints weight = 7559.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13112  Z= 0.135
  Angle     :  0.531  11.027  17569  Z= 0.272
  Chirality :  0.037   0.151   2050
  Planarity :  0.003   0.030   2230
  Dihedral  :  3.446  15.712   1731
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.29 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.22), residues: 1559
  helix:  1.57 (0.16), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.62 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  64 
 TYR   0.011   0.001   TYR I  93 
 PHE   0.018   0.001   PHE A 181 
 HIS   0.009   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (13112)
  covalent geometry    : angle       0.53127 (17569)
  hydrogen bonds       : bond        0.03076 (  724)
  hydrogen bonds       : angle       3.70673 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 178
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 ASP cc_start: 0.8952 (t70) cc_final: 0.8717 (t70)
REVERT: C   95 ARG cc_start: 0.7534 (mmt90) cc_final: 0.7017 (mmt90)
REVERT: C  146 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8175 (mtm)
REVERT: H    8 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7971 (pp30)
REVERT: H   82 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.8148 (m-70)
REVERT: H  116 MET cc_start: 0.8692 (mmt) cc_final: 0.8369 (mmt)
REVERT: J   83 LEU cc_start: 0.8517 (tp) cc_final: 0.8205 (pp)
REVERT: J  132 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8316 (mm)
REVERT: K  116 MET cc_start: 0.8082 (mtm) cc_final: 0.7695 (mtm)
REVERT: G    1 MET cc_start: 0.5923 (mmt) cc_final: 0.5574 (mmt)
REVERT: G   75 ASP cc_start: 0.7400 (p0) cc_final: 0.7052 (m-30)
  outliers start: 34
  outliers final: 23
  residues processed: 202
  average time/residue: 0.0887
  time to fit residues: 27.6270
Evaluate side-chains
  199 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  107 SER
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue    4 GLU
Chi-restraints excluded: chain I residue    6 ILE
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain J residue  132 LEU
Chi-restraints excluded: chain J residue  173 GLN
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  130 SER
Chi-restraints excluded: chain K residue  175 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue  112 LEU
Chi-restraints excluded: chain G residue  125 ILE
Chi-restraints excluded: chain F residue   15 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 129 optimal weight:    0.3980
   chunk 137 optimal weight:    0.0070
   chunk 84 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
C  35 GLN
H  88 HIS
F  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.122942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.100534 restraints weight = 29624.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.103601 restraints weight = 14295.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.105629 restraints weight = 8820.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.107009 restraints weight = 6368.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.107930 restraints weight = 5083.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.3551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13112  Z= 0.097
  Angle     :  0.505   9.364  17569  Z= 0.262
  Chirality :  0.035   0.156   2050
  Planarity :  0.002   0.032   2230
  Dihedral  :  3.397  16.700   1731
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.83 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.22), residues: 1559
  helix:  1.60 (0.16), residues: 1200
  sheet:  None (None), residues: 0
  loop : -0.57 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  85 
 TYR   0.014   0.001   TYR G  93 
 PHE   0.009   0.001   PHE B 120 
 HIS   0.008   0.000   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (13112)
  covalent geometry    : angle       0.50514 (17569)
  hydrogen bonds       : bond        0.02559 (  724)
  hydrogen bonds       : angle       3.50391 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 186
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   95 ARG cc_start: 0.7440 (mmt90) cc_final: 0.7012 (mmt90)
REVERT: H    8 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7908 (pp30)
REVERT: J   83 LEU cc_start: 0.8315 (tp) cc_final: 0.8110 (pp)
REVERT: J  132 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8309 (mm)
REVERT: K  116 MET cc_start: 0.7826 (mtm) cc_final: 0.7531 (mtm)
REVERT: G    1 MET cc_start: 0.5888 (mmt) cc_final: 0.5592 (mmt)
REVERT: G  120 MET cc_start: 0.8245 (mpp) cc_final: 0.7878 (ptp)
  outliers start: 23
  outliers final: 15
  residues processed: 202
  average time/residue: 0.0929
  time to fit residues: 28.9525
Evaluate side-chains
  188 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue    4 GLU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain J residue  132 LEU
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:    0.3980
   chunk 92 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0040
   chunk 138 optimal weight:    2.9990
   chunk 111 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 123 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 135 optimal weight:    0.9980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
C  35 GLN
H  88 HIS
F  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.101381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.078205 restraints weight = 33902.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.081187 restraints weight = 18031.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.083169 restraints weight = 12012.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.084457 restraints weight = 9145.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.085317 restraints weight = 7639.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13112  Z= 0.101
  Angle     :  0.526   8.951  17569  Z= 0.271
  Chirality :  0.036   0.152   2050
  Planarity :  0.003   0.033   2230
  Dihedral  :  3.370  19.021   1731
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 18.30 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.22), residues: 1559
  helix:  1.56 (0.16), residues: 1207
  sheet:  None (None), residues: 0
  loop : -0.56 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 122 
 TYR   0.008   0.001   TYR I  93 
 PHE   0.027   0.001   PHE C 143 
 HIS   0.009   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (13112)
  covalent geometry    : angle       0.52635 (17569)
  hydrogen bonds       : bond        0.02565 (  724)
  hydrogen bonds       : angle       3.50307 ( 2151)

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

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

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3118 Ramachandran restraints generated.
    1559 Oldfield, 0 Emsley, 1559 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8447 (mm-40)
REVERT: C   95 ARG cc_start: 0.7558 (mmt90) cc_final: 0.7006 (mmt90)
REVERT: H    8 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8060 (pp30)
REVERT: J   83 LEU cc_start: 0.8429 (tp) cc_final: 0.8136 (pp)
REVERT: J  132 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8338 (mm)
REVERT: K  116 MET cc_start: 0.7910 (mtm) cc_final: 0.7580 (mtm)
REVERT: G    1 MET cc_start: 0.6238 (mmt) cc_final: 0.5963 (mmt)
REVERT: G  120 MET cc_start: 0.8350 (mpp) cc_final: 0.7874 (ptp)
  outliers start: 17
  outliers final: 13
  residues processed: 194
  average time/residue: 0.0921
  time to fit residues: 27.4527
Evaluate side-chains
  186 residues out of total 1481 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 172
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain C residue   81 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain H residue   83 LEU
Chi-restraints excluded: chain H residue  141 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   81 THR
Chi-restraints excluded: chain I residue   88 HIS
Chi-restraints excluded: chain J residue  132 LEU
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 144 optimal weight:    2.9990
   chunk 108 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0070
   chunk 64 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9990
   chunk 155 optimal weight:    0.0770
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
C  35 GLN
H  88 HIS
F  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.099188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.076125 restraints weight = 33293.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.078977 restraints weight = 18062.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.080888 restraints weight = 12121.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.082119 restraints weight = 9297.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.082962 restraints weight = 7795.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13112  Z= 0.106
  Angle     :  0.534   8.630  17569  Z= 0.276
  Chirality :  0.036   0.148   2050
  Planarity :  0.003   0.033   2230
  Dihedral  :  3.372  18.959   1731
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 18.64 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.22), residues: 1559
  helix:  1.56 (0.16), residues: 1207
  sheet:  None (None), residues: 0
  loop : -0.53 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 122 
 TYR   0.008   0.001   TYR I  93 
 PHE   0.033   0.001   PHE C 143 
 HIS   0.009   0.001   HIS F  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (13112)
  covalent geometry    : angle       0.53353 (17569)
  hydrogen bonds       : bond        0.02559 (  724)
  hydrogen bonds       : angle       3.54933 ( 2151)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2123.89 seconds
wall clock time: 37 minutes 27.11 seconds (2247.11 seconds total)