Starting phenix.real_space_refine
on Tue Mar  3 18:13:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lo8_0935/03_2026/6lo8_0935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lo8_0935/03_2026/6lo8_0935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lo8_0935/03_2026/6lo8_0935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lo8_0935/03_2026/6lo8_0935.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lo8_0935/03_2026/6lo8_0935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lo8_0935/03_2026/6lo8_0935.map"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5075      2.51       5
     N    1348      2.21       5
     O    1486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7972
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 938
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 4, 'TRANS': 124}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1440
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 10, 'TRANS': 165}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 859
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 107}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 984
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 7, 'TRANS': 111}
    Chain: "E"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 661
          Classifications: {'peptide': 80}
          Link IDs: {'TRANS': 79}
    Chain: "F"
      Number of atoms: 660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 660
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 3, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 618
          Classifications: {'peptide': 74}
          Link IDs: {'TRANS': 73}
    Chain: "H"
      Number of atoms: 581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 581
          Classifications: {'peptide': 74}
          Link IDs: {'TRANS': 73}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "I"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 661
          Classifications: {'peptide': 80}
          Link IDs: {'TRANS': 79}
    Chain: "J"
      Number of atoms: 570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 570
          Classifications: {'peptide': 73}
          Link IDs: {'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 1.76, per 1000 atoms: 0.22
  Number of scatterers: 7972
  At special positions: 0
  Unit cell: (132.93, 104.445, 106.555, 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      63     16.00
     O    1486      8.00
     N    1348      7.00
     C    5075      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A 141 " distance=1.79
    Simple disulfide: pdb=" SG  CYS E  35 " - pdb=" SG  CYS E  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  39 " - pdb=" SG  CYS E  55 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  40 " - pdb=" SG  CYS F  66 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  44 " - pdb=" SG  CYS F  62 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  35 " - pdb=" SG  CYS G  59 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  39 " - pdb=" SG  CYS G  55 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  40 " - pdb=" SG  CYS H  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  44 " - pdb=" SG  CYS H  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  35 " - pdb=" SG  CYS I  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  39 " - pdb=" SG  CYS I  55 " distance=2.01
    Simple disulfide: pdb=" SG  CYS J  40 " - pdb=" SG  CYS J  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  44 " - pdb=" SG  CYS J  61 " distance=2.03

  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: 0.69
  Conformation dependent library (CDL) restraints added in 239.9 milliseconds
  

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1860

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      80.3% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 41
    Processing helix  chain 'A' and resid 42 through 65
      removed outlier: 3.622A  pdb=" N   SER A  46 " --> pdb=" O   CYS A  42 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   SER A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLY A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   PHE A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 146
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 3.998A  pdb=" N   PHE A 160 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 195
    Processing helix  chain 'B' and resid 37 through 62
    Processing helix  chain 'B' and resid 62 through 71
    Processing helix  chain 'B' and resid 99 through 116
      removed outlier: 4.063A  pdb=" N   TYR B 109 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 117 through 119
      No H-bonds generated for 'chain 'B' and resid 117 through 119'
    Processing helix  chain 'B' and resid 130 through 148
    Processing helix  chain 'B' and resid 244 through 261
      removed outlier: 3.607A  pdb=" N   LEU B 260 " --> pdb=" O   HIS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 394
    Processing helix  chain 'B' and resid 395 through 412
    Processing helix  chain 'C' and resid 88 through 120
      removed outlier: 4.060A  pdb=" N   PHE C 114 " --> pdb=" O   PHE C 110 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER C 117 " --> pdb=" O   LEU C 113 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY C 118 " --> pdb=" O   PHE C 114 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU C 119 " --> pdb=" O   GLY C 115 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU C 120 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 137
      removed outlier: 3.555A  pdb=" N   PHE C 137 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 167
      removed outlier: 3.959A  pdb=" N   ALA C 154 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE C 155 " --> pdb=" O   TYR C 151 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   HIS C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 174 through 198
      removed outlier: 3.598A  pdb=" N   ARG C 179 " --> pdb=" O   LYS C 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 93
      Proline residue:  D  91  - end of helix
    Processing helix  chain 'D' and resid 93 through 103
      removed outlier: 3.765A  pdb=" N   PHE D  97 " --> pdb=" O   THR D  93 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR D 102 " --> pdb=" O   TYR D  98 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY D 103 " --> pdb=" O   ALA D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 134
    Processing helix  chain 'D' and resid 140 through 166
      removed outlier: 3.784A  pdb=" N   LYS D 144 " --> pdb=" O   PRO D 140 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU D 145 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 180
    Processing helix  chain 'E' and resid 8 through 40
      removed outlier: 3.777A  pdb=" N   PHE E  12 " --> pdb=" O   GLU E   8 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   CYS E  39 " --> pdb=" O   CYS E  35 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   VAL E  40 " --> pdb=" O   PHE E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 81
      removed outlier: 3.601A  pdb=" N   ALA E  80 " --> pdb=" O   GLU E  76 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 45
      removed outlier: 3.544A  pdb=" N   THR F  32 " --> pdb=" O   ALA F  28 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   CYS F  44 " --> pdb=" O   CYS F  40 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE F  45 " --> pdb=" O   LEU F  41 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 56 through 84
      removed outlier: 4.038A  pdb=" N   GLN F  82 " --> pdb=" O   GLY F  78 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 92
    Processing helix  chain 'F' and resid 93 through 98
      removed outlier: 3.719A  pdb=" N   ARG F  97 " --> pdb=" O   HIS F  94 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 39
      removed outlier: 4.212A  pdb=" N   CYS G  39 " --> pdb=" O   CYS G  35 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 80
      removed outlier: 3.569A  pdb=" N   ALA G  80 " --> pdb=" O   GLU G  76 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 15 through 44
      removed outlier: 3.767A  pdb=" N   LEU H  26 " --> pdb=" O   ALA H  22 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   VAL H  29 " --> pdb=" O   GLU H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.596A  pdb=" N   SER H  60 " --> pdb=" O   LYS H  56 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASP H  63 " --> pdb=" O   SER H  59 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 8 through 38
    Processing helix  chain 'I' and resid 49 through 81
      removed outlier: 3.941A  pdb=" N   ALA I  80 " --> pdb=" O   GLU I  76 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU I  81 " --> pdb=" O   GLN I  77 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 15 through 44
      removed outlier: 3.758A  pdb=" N   GLU J  25 " --> pdb=" O   ALA J  21 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   CYS J  44 " --> pdb=" O   CYS J  40 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 57 through 83
      removed outlier: 4.003A  pdb=" N   ASP J  63 " --> pdb=" O   SER J  59 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLN J  81 " --> pdb=" O   GLY J  77 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   MET J  83 " --> pdb=" O   ASN J  79 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 88 through 91
    Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 241
      removed outlier: 6.975A  pdb=" N   VAL B 240 " --> pdb=" O   VAL B 373 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    611 hydrogen bonds defined for protein.
    1827 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: 1.16

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1324
        1.32 -     1.45: 2170
        1.45 -     1.57: 4530
        1.57 -     1.70: 0
        1.70 -     1.82: 93
  Bond restraints: 8117
  Sorted by residual:
  bond pdb=" N   PRO A  43 "
       pdb=" CD  PRO A  43 "
    ideal  model  delta    sigma   weight residual
    1.473  1.542 -0.069 1.40e-02 5.10e+03 2.43e+01
  bond pdb=" C   CYS I  55 "
       pdb=" O   CYS I  55 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.17e-02 7.31e+03 1.43e+01
  bond pdb=" CA  ASN G  41 "
       pdb=" C   ASN G  41 "
    ideal  model  delta    sigma   weight residual
    1.522  1.563 -0.042 1.72e-02 3.38e+03 5.85e+00
  bond pdb=" CA  CYS I  55 "
       pdb=" C   CYS I  55 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.30e-02 5.92e+03 5.05e+00
  bond pdb=" CA  ILE I  56 "
       pdb=" CB  ILE I  56 "
    ideal  model  delta    sigma   weight residual
    1.543  1.506  0.037 1.66e-02 3.63e+03 4.94e+00
  ... (remaining 8112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 10745
        2.82 -     5.64: 131
        5.64 -     8.46: 21
        8.46 -    11.28: 4
       11.28 -    14.10: 2
  Bond angle restraints: 10903
  Sorted by residual:
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     111.36  119.92   -8.56 1.09e+00 8.42e-01 6.16e+01
  angle pdb=" N   PRO A  43 "
        pdb=" CA  PRO A  43 "
        pdb=" C   PRO A  43 "
      ideal   model   delta    sigma   weight residual
     112.47   98.37   14.10 2.06e+00 2.36e-01 4.69e+01
  angle pdb=" N   CYS I  39 "
        pdb=" CA  CYS I  39 "
        pdb=" C   CYS I  39 "
      ideal   model   delta    sigma   weight residual
     112.94  122.20   -9.26 1.41e+00 5.03e-01 4.32e+01
  angle pdb=" N   ASP I  38 "
        pdb=" CA  ASP I  38 "
        pdb=" C   ASP I  38 "
      ideal   model   delta    sigma   weight residual
     111.36  118.30   -6.94 1.09e+00 8.42e-01 4.06e+01
  angle pdb=" N   CYS A  42 "
        pdb=" CA  CYS A  42 "
        pdb=" C   CYS A  42 "
      ideal   model   delta    sigma   weight residual
     109.81  122.37  -12.56 2.21e+00 2.05e-01 3.23e+01
  ... (remaining 10898 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 4298
       16.54 -    33.09: 497
       33.09 -    49.63: 95
       49.63 -    66.18: 25
       66.18 -    82.72: 13
  Dihedral angle restraints: 4928
    sinusoidal: 2038
      harmonic: 2890
  Sorted by residual:
  dihedral pdb=" CB  CYS I  39 "
           pdb=" SG  CYS I  39 "
           pdb=" SG  CYS I  55 "
           pdb=" CB  CYS I  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   15.45   77.55     1      1.00e+01 1.00e-02 7.53e+01
  dihedral pdb=" CB  CYS H  44 "
           pdb=" SG  CYS H  44 "
           pdb=" SG  CYS H  61 "
           pdb=" CB  CYS H  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.96  -75.96     1      1.00e+01 1.00e-02 7.27e+01
  dihedral pdb=" CB  CYS J  44 "
           pdb=" SG  CYS J  44 "
           pdb=" SG  CYS J  61 "
           pdb=" CB  CYS J  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.78   61.78     1      1.00e+01 1.00e-02 5.06e+01
  ... (remaining 4925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1033
       0.068 -    0.136: 130
       0.136 -    0.204: 17
       0.204 -    0.272: 3
       0.272 -    0.340: 2
  Chirality restraints: 1185
  Sorted by residual:
  chirality pdb=" CA  CYS I  39 "
            pdb=" N   CYS I  39 "
            pdb=" C   CYS I  39 "
            pdb=" CB  CYS I  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" CA  ILE I  56 "
            pdb=" N   ILE I  56 "
            pdb=" C   ILE I  56 "
            pdb=" CB  ILE I  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  CYS I  35 "
            pdb=" N   CYS I  35 "
            pdb=" C   CYS I  35 "
            pdb=" CB  CYS I  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 1182 not shown)

  Planarity restraints: 1392
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  42 "   -0.096 5.00e-02 4.00e+02   1.46e-01 3.41e+01
        pdb=" N   PRO A  43 "    0.252 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.079 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I  37 "   -0.024 2.00e-02 2.50e+03   5.06e-02 2.56e+01
        pdb=" C   THR I  37 "    0.087 2.00e-02 2.50e+03
        pdb=" O   THR I  37 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   ASP I  38 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 107 "    0.016 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   ARG B 107 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ARG B 107 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG B 108 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1389 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1694
        2.77 -     3.31: 7499
        3.31 -     3.84: 13253
        3.84 -     4.37: 14273
        4.37 -     4.90: 25404
  Nonbonded interactions: 62123
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  71 "
            pdb=" O   SER D 128 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   MET A  36 "
            pdb=" OG1 THR A  40 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   GLU I  33 "
            pdb=" OG1 THR I  37 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OH  TYR A 136 "
            pdb=" OG  SER A 186 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   ASP E  42 "
            pdb=" NZ  LYS J  68 "
     model   vdw
     2.318 3.120
  ... (remaining 62118 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 'E' and resid 7 through 80)
  selection = chain 'G'
  selection = (chain 'I' and resid 7 through 80)
}
ncs_group {
  reference = (chain 'H' and resid 14 through 86)
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.990
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
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      :  0.006   0.246   8130  Z= 0.285
  Angle     :  0.938  29.165  10929  Z= 0.525
  Chirality :  0.049   0.340   1185
  Planarity :  0.007   0.146   1392
  Dihedral  : 14.877  82.722   3029
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.72 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  7.10 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.08 (0.21), residues: 967
  helix: -1.56 (0.14), residues: 753
  sheet: -0.91 (0.97), residues: 22
  loop : -3.38 (0.34), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  73 
 TYR   0.014   0.002   TYR C 133 
 PHE   0.023   0.002   PHE D  65 
 TRP   0.011   0.001   TRP B 106 
 HIS   0.009   0.002   HIS C 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 8117)
  covalent geometry    : angle       0.86502 (10903)
  SS BOND              : bond        0.06854 (   13)
  SS BOND              : angle       7.51084 (   26)
  hydrogen bonds       : bond        0.10768 (  611)
  hydrogen bonds       : angle       6.13108 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 332
  time to evaluate  : 0.308 
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: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8288 (mp) cc_final: 0.8030 (pp)
REVERT: A  129 PHE cc_start: 0.7855 (m-80) cc_final: 0.7170 (m-10)
REVERT: A  189 ILE cc_start: 0.9155 (mm) cc_final: 0.8867 (mm)
REVERT: B   39 MET cc_start: 0.4281 (mtm) cc_final: 0.3602 (tmm)
REVERT: B   42 TRP cc_start: 0.7701 (m100) cc_final: 0.7003 (m-10)
REVERT: B   82 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7807 (tptt)
REVERT: C  108 TYR cc_start: 0.8142 (m-80) cc_final: 0.7629 (m-80)
REVERT: C  175 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8645 (tttt)
REVERT: D   82 GLU cc_start: 0.8368 (tp30) cc_final: 0.8101 (tp30)
REVERT: D  123 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: D  130 ILE cc_start: 0.9328 (tt) cc_final: 0.9128 (tt)
REVERT: D  165 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8446 (mm-30)
REVERT: G   28 TYR cc_start: 0.8880 (t80) cc_final: 0.8585 (t80)
REVERT: H   19 ILE cc_start: 0.9291 (tt) cc_final: 0.8881 (tp)
REVERT: H   36 LEU cc_start: 0.9542 (tp) cc_final: 0.9313 (tp)
REVERT: H   39 ASN cc_start: 0.8650 (m-40) cc_final: 0.7616 (m110)
REVERT: I   17 GLU cc_start: 0.8570 (tp30) cc_final: 0.8214 (tp30)
REVERT: I   19 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8708 (mtpp)
  outliers start: 4
  outliers final: 2
  residues processed: 336
  average time/residue: 0.1066
  time to fit residues: 45.8946
Evaluate side-chains
  232 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 230
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain I residue   35 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
A 154 ASN
B 135 ASN
C 156 HIS
F  34 ASN
F  90 ASN
F  91 GLN
G  20 GLN
G  30 ASN
G  53 GLN
G  77 GLN
** H  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  30 ASN
J  20 GLN
J  34 ASN
** J  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  75 GLN
J  85 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.074548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.060515 restraints weight = 29848.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.062197 restraints weight = 16407.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.063320 restraints weight = 10953.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.064028 restraints weight = 8376.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.064369 restraints weight = 7080.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.112   8130  Z= 0.162
  Angle     :  0.731  14.494  10929  Z= 0.384
  Chirality :  0.040   0.194   1185
  Planarity :  0.005   0.092   1392
  Dihedral  :  5.557  53.438   1075
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.83 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.92 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.25), residues: 967
  helix:  0.38 (0.17), residues: 762
  sheet:  0.16 (1.07), residues: 22
  loop : -3.05 (0.37), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  69 
 TYR   0.020   0.001   TYR H  49 
 PHE   0.012   0.001   PHE A 182 
 TRP   0.009   0.001   TRP B 106 
 HIS   0.004   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8117)
  covalent geometry    : angle       0.71730 (10903)
  SS BOND              : bond        0.00653 (   13)
  SS BOND              : angle       2.97903 (   26)
  hydrogen bonds       : bond        0.04620 (  611)
  hydrogen bonds       : angle       4.48260 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 269
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7222 (tm-30)
REVERT: A   56 LEU cc_start: 0.8245 (mp) cc_final: 0.8003 (pp)
REVERT: A  129 PHE cc_start: 0.7960 (m-80) cc_final: 0.7329 (m-80)
REVERT: B   39 MET cc_start: 0.3828 (mtm) cc_final: 0.3409 (tmm)
REVERT: B   67 THR cc_start: 0.8494 (m) cc_final: 0.8100 (p)
REVERT: B   82 LYS cc_start: 0.8083 (mmpt) cc_final: 0.7682 (tptt)
REVERT: C  103 MET cc_start: 0.8317 (mtt) cc_final: 0.8102 (mtt)
REVERT: D   64 MET cc_start: 0.6516 (tmm) cc_final: 0.6127 (tmm)
REVERT: D  111 ASP cc_start: 0.7458 (t0) cc_final: 0.6929 (t0)
REVERT: D  123 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8074 (tm-30)
REVERT: D  144 LYS cc_start: 0.8392 (tttt) cc_final: 0.8088 (pttm)
REVERT: D  155 MET cc_start: 0.7852 (mmp) cc_final: 0.7600 (mmt)
REVERT: D  165 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8378 (mm-30)
REVERT: E   11 GLU cc_start: 0.8191 (mp0) cc_final: 0.7980 (mp0)
REVERT: E   64 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8195 (mm)
REVERT: F   27 ASP cc_start: 0.8823 (m-30) cc_final: 0.8361 (m-30)
REVERT: F   35 ASN cc_start: 0.8916 (t0) cc_final: 0.8685 (t0)
REVERT: G   22 LYS cc_start: 0.8897 (tptp) cc_final: 0.8562 (tptt)
REVERT: G   28 TYR cc_start: 0.8858 (t80) cc_final: 0.8642 (t80)
REVERT: I   17 GLU cc_start: 0.8698 (tp30) cc_final: 0.8398 (tp30)
REVERT: I   19 LYS cc_start: 0.9311 (mmtt) cc_final: 0.8853 (mtpp)
REVERT: I   35 CYS cc_start: 0.6154 (m) cc_final: 0.5916 (m)
REVERT: J   23 GLU cc_start: 0.8202 (tp30) cc_final: 0.7648 (mm-30)
REVERT: J   80 MET cc_start: 0.8102 (mmp) cc_final: 0.7869 (mmp)
  outliers start: 28
  outliers final: 14
  residues processed: 285
  average time/residue: 0.0898
  time to fit residues: 33.3975
Evaluate side-chains
  246 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 231
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   51 LYS
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 78 optimal weight:    0.8980
   chunk 3 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D 168 ASN
F  94 HIS
G  20 GLN
** H  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.074387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.060552 restraints weight = 29468.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.062170 restraints weight = 16447.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.063253 restraints weight = 11046.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.063884 restraints weight = 8519.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.064363 restraints weight = 7293.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   8130  Z= 0.154
  Angle     :  0.704  15.305  10929  Z= 0.368
  Chirality :  0.039   0.176   1185
  Planarity :  0.004   0.072   1392
  Dihedral  :  5.068  44.398   1073
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.93 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 18.33 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.26), residues: 967
  helix:  1.09 (0.18), residues: 762
  sheet:  0.17 (1.05), residues: 22
  loop : -2.87 (0.40), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  26 
 TYR   0.015   0.001   TYR E  28 
 PHE   0.024   0.001   PHE C 187 
 TRP   0.007   0.001   TRP B 106 
 HIS   0.005   0.001   HIS E  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 8117)
  covalent geometry    : angle       0.69258 (10903)
  SS BOND              : bond        0.00368 (   13)
  SS BOND              : angle       2.69961 (   26)
  hydrogen bonds       : bond        0.04430 (  611)
  hydrogen bonds       : angle       4.26197 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 256
  time to evaluate  : 0.303 
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: symmetry clash
REVERT: A   56 LEU cc_start: 0.8178 (mp) cc_final: 0.7904 (pp)
REVERT: A  129 PHE cc_start: 0.7892 (m-80) cc_final: 0.7215 (m-10)
REVERT: A  134 MET cc_start: 0.8665 (tpp) cc_final: 0.8342 (tpt)
REVERT: A  140 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7824 (tm-30)
REVERT: A  194 LYS cc_start: 0.8850 (tppp) cc_final: 0.8584 (mptt)
REVERT: B   39 MET cc_start: 0.3979 (mtm) cc_final: 0.3500 (tmm)
REVERT: B   82 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7735 (tptt)
REVERT: C  163 HIS cc_start: 0.8781 (t70) cc_final: 0.8258 (t70)
REVERT: D   64 MET cc_start: 0.6414 (tmm) cc_final: 0.6039 (tmm)
REVERT: D   78 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: D  111 ASP cc_start: 0.7699 (t0) cc_final: 0.7105 (t0)
REVERT: D  123 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: D  144 LYS cc_start: 0.8443 (tttt) cc_final: 0.8186 (pttm)
REVERT: D  165 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8184 (mm-30)
REVERT: E   18 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7920 (mp10)
REVERT: E   64 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8255 (mm)
REVERT: F   27 ASP cc_start: 0.8756 (m-30) cc_final: 0.8405 (m-30)
REVERT: F   35 ASN cc_start: 0.8952 (t0) cc_final: 0.8704 (t0)
REVERT: G   28 TYR cc_start: 0.8830 (t80) cc_final: 0.8629 (t80)
REVERT: H   59 SER cc_start: 0.8587 (m) cc_final: 0.7903 (p)
REVERT: H   62 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8707 (mm)
REVERT: I   10 GLN cc_start: 0.8815 (mp10) cc_final: 0.8529 (pm20)
REVERT: I   11 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7399 (mp0)
REVERT: I   17 GLU cc_start: 0.8657 (tp30) cc_final: 0.8362 (tp30)
REVERT: J   80 MET cc_start: 0.7962 (mmp) cc_final: 0.7733 (mmp)
  outliers start: 30
  outliers final: 18
  residues processed: 272
  average time/residue: 0.1021
  time to fit residues: 36.2865
Evaluate side-chains
  254 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 232
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue   11 GLU
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
E  13 GLN
G  20 GLN
H  79 ASN
I  30 ASN
** J  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.074572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.060774 restraints weight = 30038.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.062388 restraints weight = 16685.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.063452 restraints weight = 11203.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.064174 restraints weight = 8656.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.064503 restraints weight = 7321.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8130  Z= 0.150
  Angle     :  0.695  10.869  10929  Z= 0.363
  Chirality :  0.040   0.244   1185
  Planarity :  0.004   0.062   1392
  Dihedral  :  5.047  46.397   1073
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 19.93 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.26), residues: 967
  helix:  1.39 (0.18), residues: 757
  sheet:  0.11 (1.05), residues: 22
  loop : -2.69 (0.39), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  26 
 TYR   0.020   0.001   TYR C 151 
 PHE   0.032   0.001   PHE C 107 
 TRP   0.006   0.001   TRP B 106 
 HIS   0.004   0.001   HIS F  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8117)
  covalent geometry    : angle       0.68548 (10903)
  SS BOND              : bond        0.00317 (   13)
  SS BOND              : angle       2.43849 (   26)
  hydrogen bonds       : bond        0.04440 (  611)
  hydrogen bonds       : angle       4.24422 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 261
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: A   56 LEU cc_start: 0.8208 (mp) cc_final: 0.7885 (pp)
REVERT: A  140 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7799 (tm-30)
REVERT: A  194 LYS cc_start: 0.8828 (tppp) cc_final: 0.8586 (mptt)
REVERT: B   39 MET cc_start: 0.3941 (mtm) cc_final: 0.3456 (tmm)
REVERT: B   82 LYS cc_start: 0.8146 (mmpt) cc_final: 0.7892 (tptt)
REVERT: C  163 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8084 (t70)
REVERT: D   78 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7818 (tm-30)
REVERT: D  111 ASP cc_start: 0.7857 (t0) cc_final: 0.7400 (t0)
REVERT: D  118 PHE cc_start: 0.8733 (t80) cc_final: 0.8524 (t80)
REVERT: D  123 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: D  155 MET cc_start: 0.7589 (mmt) cc_final: 0.7364 (mmp)
REVERT: D  165 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8220 (mm-30)
REVERT: E   64 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8298 (mm)
REVERT: E   73 ARG cc_start: 0.7812 (tpp-160) cc_final: 0.7550 (ttm-80)
REVERT: F   27 ASP cc_start: 0.8722 (m-30) cc_final: 0.8340 (m-30)
REVERT: F   29 MET cc_start: 0.7792 (mtt) cc_final: 0.7524 (mtt)
REVERT: F   60 GLN cc_start: 0.8396 (mt0) cc_final: 0.7784 (mp10)
REVERT: F   84 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8230 (tpp80)
REVERT: G   28 TYR cc_start: 0.8803 (t80) cc_final: 0.8516 (t80)
REVERT: G   42 ASP cc_start: 0.7512 (t0) cc_final: 0.7150 (t0)
REVERT: G   52 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7758 (mt-10)
REVERT: H   59 SER cc_start: 0.8550 (m) cc_final: 0.7877 (p)
REVERT: H   62 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8665 (mm)
REVERT: I    7 LYS cc_start: 0.8789 (ptmm) cc_final: 0.8230 (tmmt)
REVERT: I   10 GLN cc_start: 0.8800 (mp10) cc_final: 0.7710 (pm20)
REVERT: I   11 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7229 (mp0)
REVERT: I   17 GLU cc_start: 0.8636 (tp30) cc_final: 0.8318 (tp30)
REVERT: I   19 LYS cc_start: 0.9468 (mtpp) cc_final: 0.9213 (mtpp)
  outliers start: 34
  outliers final: 19
  residues processed: 281
  average time/residue: 0.1013
  time to fit residues: 37.4440
Evaluate side-chains
  252 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 229
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   66 HIS
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue   11 GLU
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 91 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 68 optimal weight:    0.3980
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
H  75 GLN
** I  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  39 ASN ** 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 = 0.3522 r_free = 0.3522 target = 0.074831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.061057 restraints weight = 30022.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.062689 restraints weight = 17177.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.063779 restraints weight = 11562.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.064511 restraints weight = 8861.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.064874 restraints weight = 7428.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8130  Z= 0.154
  Angle     :  0.723  11.524  10929  Z= 0.376
  Chirality :  0.040   0.238   1185
  Planarity :  0.004   0.063   1392
  Dihedral  :  5.002  46.939   1073
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.14 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.79 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.26), residues: 967
  helix:  1.52 (0.18), residues: 758
  sheet:  0.13 (1.05), residues: 22
  loop : -2.55 (0.39), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  26 
 TYR   0.023   0.001   TYR C 151 
 PHE   0.031   0.001   PHE C 107 
 TRP   0.007   0.000   TRP B 106 
 HIS   0.006   0.001   HIS F  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 8117)
  covalent geometry    : angle       0.71118 (10903)
  SS BOND              : bond        0.00406 (   13)
  SS BOND              : angle       2.74905 (   26)
  hydrogen bonds       : bond        0.04433 (  611)
  hydrogen bonds       : angle       4.21898 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 251
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7440 (tm-30)
REVERT: A  140 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7787 (tm-30)
REVERT: A  194 LYS cc_start: 0.8835 (tppp) cc_final: 0.8605 (mptt)
REVERT: B   39 MET cc_start: 0.4007 (mtm) cc_final: 0.3489 (tmm)
REVERT: C  163 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.8157 (t70)
REVERT: D   64 MET cc_start: 0.6137 (tmm) cc_final: 0.5807 (tmm)
REVERT: D   78 GLN cc_start: 0.8427 (tm-30) cc_final: 0.7873 (tm-30)
REVERT: D  111 ASP cc_start: 0.7858 (t0) cc_final: 0.7278 (t0)
REVERT: D  118 PHE cc_start: 0.8735 (t80) cc_final: 0.8473 (t80)
REVERT: D  123 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8147 (tm-30)
REVERT: D  155 MET cc_start: 0.7612 (mmt) cc_final: 0.7407 (mmp)
REVERT: D  165 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7978 (mm-30)
REVERT: E   64 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8472 (mm)
REVERT: F   27 ASP cc_start: 0.8664 (m-30) cc_final: 0.8335 (m-30)
REVERT: F   60 GLN cc_start: 0.8381 (mt0) cc_final: 0.7964 (mt0)
REVERT: F   84 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8131 (tpp80)
REVERT: G   28 TYR cc_start: 0.8797 (t80) cc_final: 0.8550 (t80)
REVERT: G   42 ASP cc_start: 0.7625 (t0) cc_final: 0.7277 (t0)
REVERT: H   39 ASN cc_start: 0.8187 (m110) cc_final: 0.5889 (m110)
REVERT: H   59 SER cc_start: 0.8664 (m) cc_final: 0.8090 (p)
REVERT: H   62 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8662 (mm)
REVERT: I    7 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8185 (tmmt)
REVERT: I   10 GLN cc_start: 0.8541 (mp10) cc_final: 0.7771 (pm20)
REVERT: I   19 LYS cc_start: 0.9457 (mtpp) cc_final: 0.9196 (mtpp)
REVERT: J   23 GLU cc_start: 0.8562 (tp30) cc_final: 0.8281 (mm-30)
  outliers start: 33
  outliers final: 20
  residues processed: 266
  average time/residue: 0.0956
  time to fit residues: 33.4254
Evaluate side-chains
  250 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 227
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 86 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
H  75 GLN
I  66 HIS
J  39 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.074837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.061202 restraints weight = 29797.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.062790 restraints weight = 16545.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.063881 restraints weight = 11220.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.064479 restraints weight = 8625.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.064825 restraints weight = 7380.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8130  Z= 0.158
  Angle     :  0.724  11.478  10929  Z= 0.375
  Chirality :  0.041   0.231   1185
  Planarity :  0.004   0.064   1392
  Dihedral  :  4.982  45.859   1073
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 22.79 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.26), residues: 967
  helix:  1.55 (0.18), residues: 758
  sheet:  0.09 (1.04), residues: 22
  loop : -2.52 (0.39), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG I  26 
 TYR   0.026   0.001   TYR C 151 
 PHE   0.034   0.001   PHE C 107 
 TRP   0.006   0.001   TRP B 106 
 HIS   0.004   0.001   HIS F  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8117)
  covalent geometry    : angle       0.71441 (10903)
  SS BOND              : bond        0.00442 (   13)
  SS BOND              : angle       2.54099 (   26)
  hydrogen bonds       : bond        0.04429 (  611)
  hydrogen bonds       : angle       4.19500 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 250
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7430 (tm-30)
REVERT: A  140 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7747 (tm-30)
REVERT: A  194 LYS cc_start: 0.8902 (tppp) cc_final: 0.8634 (mptt)
REVERT: B   39 MET cc_start: 0.4093 (mtm) cc_final: 0.3534 (tmm)
REVERT: B   67 THR cc_start: 0.8446 (m) cc_final: 0.8190 (p)
REVERT: C  163 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8122 (t70)
REVERT: D   64 MET cc_start: 0.6111 (tmm) cc_final: 0.5729 (tmm)
REVERT: D   78 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7878 (tm-30)
REVERT: D  111 ASP cc_start: 0.7954 (t0) cc_final: 0.7331 (t0)
REVERT: D  118 PHE cc_start: 0.8678 (t80) cc_final: 0.8376 (t80)
REVERT: D  123 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: D  155 MET cc_start: 0.7613 (mmt) cc_final: 0.7386 (mmp)
REVERT: D  165 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8015 (mm-30)
REVERT: E   52 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8025 (mp0)
REVERT: E   64 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8438 (mm)
REVERT: F   27 ASP cc_start: 0.8718 (m-30) cc_final: 0.8359 (m-30)
REVERT: F   60 GLN cc_start: 0.8415 (mt0) cc_final: 0.8000 (mt0)
REVERT: G   28 TYR cc_start: 0.8812 (t80) cc_final: 0.8548 (t80)
REVERT: G   42 ASP cc_start: 0.7620 (t0) cc_final: 0.7256 (t0)
REVERT: H   59 SER cc_start: 0.8708 (m) cc_final: 0.8172 (p)
REVERT: H   62 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8646 (mm)
REVERT: I    7 LYS cc_start: 0.8706 (ptmm) cc_final: 0.8357 (tmmt)
REVERT: I   10 GLN cc_start: 0.8525 (mp10) cc_final: 0.7840 (pm20)
REVERT: I   11 GLU cc_start: 0.7739 (mp0) cc_final: 0.7364 (mp0)
REVERT: I   19 LYS cc_start: 0.9478 (mtpp) cc_final: 0.9219 (mtpp)
REVERT: I   26 ARG cc_start: 0.7524 (tmt-80) cc_final: 0.7051 (tmt-80)
REVERT: I   33 GLU cc_start: 0.8398 (tp30) cc_final: 0.7936 (tp30)
  outliers start: 36
  outliers final: 23
  residues processed: 264
  average time/residue: 0.0821
  time to fit residues: 29.0692
Evaluate side-chains
  254 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 227
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain G residue   66 HIS
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    0.1980
   chunk 49 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
H  39 ASN
H  46 ASN
I  30 ASN
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.074414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.061694 restraints weight = 30666.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.063225 restraints weight = 15865.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.063640 restraints weight = 11546.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.063752 restraints weight = 8952.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.063899 restraints weight = 8651.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8130  Z= 0.177
  Angle     :  0.749  11.690  10929  Z= 0.389
  Chirality :  0.041   0.255   1185
  Planarity :  0.004   0.067   1392
  Dihedral  :  5.013  43.689   1073
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.86 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 24.86 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.26), residues: 967
  helix:  1.62 (0.18), residues: 759
  sheet:  0.03 (1.04), residues: 22
  loop : -2.49 (0.40), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  26 
 TYR   0.028   0.001   TYR C 151 
 PHE   0.035   0.001   PHE C 107 
 TRP   0.006   0.001   TRP B 106 
 HIS   0.006   0.001   HIS I  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 8117)
  covalent geometry    : angle       0.74067 (10903)
  SS BOND              : bond        0.00636 (   13)
  SS BOND              : angle       2.42526 (   26)
  hydrogen bonds       : bond        0.04423 (  611)
  hydrogen bonds       : angle       4.20167 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 234
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: A  140 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: A  194 LYS cc_start: 0.8907 (tppp) cc_final: 0.8627 (mptt)
REVERT: B   39 MET cc_start: 0.4130 (mtm) cc_final: 0.3565 (tmm)
REVERT: B   67 THR cc_start: 0.8510 (m) cc_final: 0.8246 (p)
REVERT: C  163 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8189 (t70)
REVERT: D   64 MET cc_start: 0.6380 (tmm) cc_final: 0.6087 (tmm)
REVERT: D   78 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: D  111 ASP cc_start: 0.8078 (t0) cc_final: 0.7477 (t0)
REVERT: D  118 PHE cc_start: 0.8668 (t80) cc_final: 0.8418 (t80)
REVERT: D  123 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: D  155 MET cc_start: 0.7724 (mmt) cc_final: 0.7510 (mmp)
REVERT: D  165 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7964 (mm-30)
REVERT: E   52 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8027 (mp0)
REVERT: E   64 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8292 (mm)
REVERT: F   27 ASP cc_start: 0.8717 (m-30) cc_final: 0.8327 (m-30)
REVERT: F   60 GLN cc_start: 0.8420 (mt0) cc_final: 0.7781 (mp10)
REVERT: G   28 TYR cc_start: 0.8833 (t80) cc_final: 0.8581 (t80)
REVERT: G   42 ASP cc_start: 0.7604 (t0) cc_final: 0.7229 (t0)
REVERT: H   59 SER cc_start: 0.8746 (m) cc_final: 0.8254 (p)
REVERT: H   62 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8658 (mm)
REVERT: I    7 LYS cc_start: 0.8752 (ptmm) cc_final: 0.8409 (tmmt)
REVERT: I   10 GLN cc_start: 0.8567 (mp10) cc_final: 0.7815 (pm20)
REVERT: I   11 GLU cc_start: 0.7864 (mp0) cc_final: 0.7443 (mp0)
REVERT: I   19 LYS cc_start: 0.9412 (mtpp) cc_final: 0.9156 (mtpp)
REVERT: J   23 GLU cc_start: 0.8788 (tp30) cc_final: 0.8588 (tp30)
  outliers start: 36
  outliers final: 25
  residues processed: 251
  average time/residue: 0.0878
  time to fit residues: 29.6835
Evaluate side-chains
  254 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 225
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain G residue   66 HIS
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
D 168 ASN
H  39 ASN
H  79 ASN
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.074698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.061044 restraints weight = 30157.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.062655 restraints weight = 16822.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.063718 restraints weight = 11367.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.064304 restraints weight = 8825.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.064889 restraints weight = 7584.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.4407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8130  Z= 0.164
  Angle     :  0.754  12.300  10929  Z= 0.391
  Chirality :  0.041   0.233   1185
  Planarity :  0.004   0.064   1392
  Dihedral  :  5.024  44.768   1073
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.76 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 25.09 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.26), residues: 967
  helix:  1.66 (0.18), residues: 759
  sheet:  0.15 (1.04), residues: 22
  loop : -2.43 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  26 
 TYR   0.033   0.001   TYR C 151 
 PHE   0.035   0.001   PHE C 107 
 TRP   0.006   0.001   TRP B 106 
 HIS   0.005   0.001   HIS I  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 8117)
  covalent geometry    : angle       0.74339 (10903)
  SS BOND              : bond        0.00520 (   13)
  SS BOND              : angle       2.66125 (   26)
  hydrogen bonds       : bond        0.04383 (  611)
  hydrogen bonds       : angle       4.21738 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 240
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7407 (tm-30)
REVERT: A   45 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8293 (mmtm)
REVERT: A  140 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7676 (tm-30)
REVERT: A  194 LYS cc_start: 0.8888 (tppp) cc_final: 0.8643 (mptt)
REVERT: B   39 MET cc_start: 0.4027 (mtm) cc_final: 0.3516 (tmm)
REVERT: C  163 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.7998 (t70)
REVERT: D   64 MET cc_start: 0.6195 (tmm) cc_final: 0.5865 (tmm)
REVERT: D   78 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: D  111 ASP cc_start: 0.8071 (t0) cc_final: 0.7444 (t0)
REVERT: D  118 PHE cc_start: 0.8637 (t80) cc_final: 0.8386 (t80)
REVERT: D  123 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8218 (tm-30)
REVERT: D  155 MET cc_start: 0.7685 (mmt) cc_final: 0.7478 (mmp)
REVERT: D  165 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7919 (mm-30)
REVERT: E   52 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7951 (mp0)
REVERT: E   64 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8259 (mm)
REVERT: E   73 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7731 (ttm-80)
REVERT: F   27 ASP cc_start: 0.8669 (m-30) cc_final: 0.8412 (m-30)
REVERT: F   60 GLN cc_start: 0.8413 (mt0) cc_final: 0.7983 (mt0)
REVERT: G   28 TYR cc_start: 0.8764 (t80) cc_final: 0.8516 (t80)
REVERT: G   42 ASP cc_start: 0.7621 (t0) cc_final: 0.7243 (t0)
REVERT: H   59 SER cc_start: 0.8680 (m) cc_final: 0.8163 (p)
REVERT: H   62 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8613 (mm)
REVERT: I    7 LYS cc_start: 0.8626 (ptmm) cc_final: 0.8247 (tmmt)
REVERT: I   10 GLN cc_start: 0.8500 (mp10) cc_final: 0.7756 (pm20)
REVERT: I   11 GLU cc_start: 0.7837 (mp0) cc_final: 0.7464 (mp0)
REVERT: I   19 LYS cc_start: 0.9401 (mtpp) cc_final: 0.9119 (mtpp)
  outliers start: 37
  outliers final: 27
  residues processed: 256
  average time/residue: 0.0918
  time to fit residues: 31.3372
Evaluate side-chains
  259 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 228
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  157 THR
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   55 CYS
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain G residue   66 HIS
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue   21 MET
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 82 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   chunk 79 optimal weight:    0.8980
   chunk 80 optimal weight:    0.0040
   chunk 68 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.075394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.061677 restraints weight = 29762.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.063320 restraints weight = 16546.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.064305 restraints weight = 11205.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.065086 restraints weight = 8800.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.065355 restraints weight = 7428.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8130  Z= 0.154
  Angle     :  0.780  13.747  10929  Z= 0.400
  Chirality :  0.042   0.367   1185
  Planarity :  0.004   0.065   1392
  Dihedral  :  4.940  44.914   1073
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.12 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.26), residues: 967
  helix:  1.70 (0.18), residues: 760
  sheet:  0.21 (1.06), residues: 22
  loop : -2.47 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG I  26 
 TYR   0.044   0.001   TYR C 151 
 PHE   0.033   0.001   PHE C 107 
 TRP   0.007   0.001   TRP B 106 
 HIS   0.006   0.001   HIS I  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8117)
  covalent geometry    : angle       0.77499 (10903)
  SS BOND              : bond        0.00347 (   13)
  SS BOND              : angle       2.03571 (   26)
  hydrogen bonds       : bond        0.04368 (  611)
  hydrogen bonds       : angle       4.25121 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 236
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7390 (tm-30)
REVERT: A   45 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8181 (mmtm)
REVERT: A  140 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7612 (tm-30)
REVERT: A  194 LYS cc_start: 0.8887 (tppp) cc_final: 0.8639 (mptt)
REVERT: B   39 MET cc_start: 0.4101 (mtm) cc_final: 0.3582 (tmm)
REVERT: C  163 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8062 (t70)
REVERT: D   64 MET cc_start: 0.6052 (tmm) cc_final: 0.5751 (tmm)
REVERT: D   78 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7904 (tm-30)
REVERT: D  111 ASP cc_start: 0.8056 (t0) cc_final: 0.7446 (t0)
REVERT: D  118 PHE cc_start: 0.8605 (t80) cc_final: 0.8380 (t80)
REVERT: D  123 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: D  155 MET cc_start: 0.7682 (mmt) cc_final: 0.7478 (mmp)
REVERT: D  165 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: E   52 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.7916 (mp0)
REVERT: E   64 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8255 (mm)
REVERT: F   27 ASP cc_start: 0.8695 (m-30) cc_final: 0.8485 (m-30)
REVERT: F   60 GLN cc_start: 0.8385 (mt0) cc_final: 0.7966 (mt0)
REVERT: G   42 ASP cc_start: 0.7578 (t0) cc_final: 0.7243 (t0)
REVERT: H   59 SER cc_start: 0.8675 (m) cc_final: 0.8187 (p)
REVERT: H   62 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8504 (mm)
REVERT: I    7 LYS cc_start: 0.8544 (ptmm) cc_final: 0.8156 (tmmt)
REVERT: I   10 GLN cc_start: 0.8538 (mp10) cc_final: 0.7741 (pm20)
REVERT: I   11 GLU cc_start: 0.7868 (mp0) cc_final: 0.7477 (mp0)
REVERT: I   19 LYS cc_start: 0.9348 (mtpp) cc_final: 0.9114 (mtpp)
  outliers start: 32
  outliers final: 24
  residues processed: 253
  average time/residue: 0.0941
  time to fit residues: 31.8778
Evaluate side-chains
  257 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 229
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   55 CYS
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue   33 GLU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   59 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 21 optimal weight:    0.0000
   chunk 66 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0770
   chunk 72 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.6944

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.075148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.061568 restraints weight = 29921.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.063244 restraints weight = 16878.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.064264 restraints weight = 11352.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.065032 restraints weight = 8844.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.065471 restraints weight = 7424.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8130  Z= 0.158
  Angle     :  0.786  13.206  10929  Z= 0.405
  Chirality :  0.042   0.329   1185
  Planarity :  0.004   0.066   1392
  Dihedral  :  4.876  42.082   1073
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 26.80 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.26), residues: 967
  helix:  1.73 (0.18), residues: 760
  sheet:  0.25 (1.07), residues: 22
  loop : -2.46 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG I  26 
 TYR   0.037   0.001   TYR C 151 
 PHE   0.032   0.001   PHE C 107 
 TRP   0.006   0.001   TRP B 106 
 HIS   0.008   0.001   HIS I  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8117)
  covalent geometry    : angle       0.78085 (10903)
  SS BOND              : bond        0.00350 (   13)
  SS BOND              : angle       1.95987 (   26)
  hydrogen bonds       : bond        0.04333 (  611)
  hydrogen bonds       : angle       4.27600 ( 1827)

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7390 (tm-30)
REVERT: A   45 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8267 (mptt)
REVERT: A  140 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7546 (tm-30)
REVERT: A  194 LYS cc_start: 0.8883 (tppp) cc_final: 0.8637 (mptt)
REVERT: B   39 MET cc_start: 0.3991 (mtm) cc_final: 0.3517 (tmm)
REVERT: C  108 TYR cc_start: 0.8079 (m-80) cc_final: 0.7689 (m-80)
REVERT: C  163 HIS cc_start: 0.8531 (OUTLIER) cc_final: 0.8052 (t70)
REVERT: D   64 MET cc_start: 0.5751 (tmm) cc_final: 0.5435 (tmm)
REVERT: D   78 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: D  111 ASP cc_start: 0.8097 (t0) cc_final: 0.7467 (t0)
REVERT: D  118 PHE cc_start: 0.8611 (t80) cc_final: 0.8382 (t80)
REVERT: D  123 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8224 (tm-30)
REVERT: D  155 MET cc_start: 0.7699 (mmt) cc_final: 0.7475 (mmp)
REVERT: D  165 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8001 (mm-30)
REVERT: E   52 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7922 (mp0)
REVERT: E   64 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8245 (mm)
REVERT: F   27 ASP cc_start: 0.8741 (m-30) cc_final: 0.8495 (m-30)
REVERT: F   60 GLN cc_start: 0.8367 (mt0) cc_final: 0.7938 (mt0)
REVERT: G   42 ASP cc_start: 0.7639 (t0) cc_final: 0.7254 (t0)
REVERT: H   59 SER cc_start: 0.8678 (m) cc_final: 0.8207 (p)
REVERT: H   62 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8534 (mm)
REVERT: I    7 LYS cc_start: 0.8519 (ptmm) cc_final: 0.8146 (tmmt)
REVERT: I   10 GLN cc_start: 0.8495 (mp10) cc_final: 0.7684 (pm20)
REVERT: I   11 GLU cc_start: 0.7798 (mp0) cc_final: 0.7422 (mp0)
REVERT: I   19 LYS cc_start: 0.9358 (mtpp) cc_final: 0.9113 (tppp)
  outliers start: 26
  outliers final: 22
  residues processed: 249
  average time/residue: 0.0941
  time to fit residues: 31.2230
Evaluate side-chains
  253 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 227
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   55 CYS
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0770
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.075690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.062111 restraints weight = 29728.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.063755 restraints weight = 16550.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.064878 restraints weight = 11208.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.065526 restraints weight = 8615.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.066043 restraints weight = 7338.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8130  Z= 0.158
  Angle     :  0.808  13.286  10929  Z= 0.415
  Chirality :  0.042   0.303   1185
  Planarity :  0.004   0.068   1392
  Dihedral  :  4.855  42.119   1073
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 26.92 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.40 (0.26), residues: 967
  helix:  1.71 (0.18), residues: 765
  sheet:  0.30 (1.07), residues: 22
  loop : -2.49 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG I  26 
 TYR   0.036   0.001   TYR C 151 
 PHE   0.031   0.001   PHE C 107 
 TRP   0.007   0.001   TRP B 106 
 HIS   0.008   0.001   HIS I  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8117)
  covalent geometry    : angle       0.80307 (10903)
  SS BOND              : bond        0.00328 (   13)
  SS BOND              : angle       1.93892 (   26)
  hydrogen bonds       : bond        0.04366 (  611)
  hydrogen bonds       : angle       4.29454 ( 1827)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1480.77 seconds
wall clock time: 26 minutes 14.61 seconds (1574.61 seconds total)