Starting phenix.real_space_refine
on Wed Jul 30 15:13:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6c0w_7326/07_2025/6c0w_7326_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6c0w_7326/07_2025/6c0w_7326.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6c0w_7326/07_2025/6c0w_7326.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6c0w_7326/07_2025/6c0w_7326.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6c0w_7326/07_2025/6c0w_7326_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6c0w_7326/07_2025/6c0w_7326_neut.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     278      5.49       5
     S      16      5.16       5
     C    7427      2.51       5
     N    2429      2.21       5
     O    2972      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13122
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 732
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "B"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 634
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 764
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 749
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "F"
      Number of atoms: 623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 623
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 771
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2835
          Classifications: {'DNA': 139}
          Link IDs: {'rna3p': 138}
    Chain: "J"
      Number of atoms: 2864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2864
          Classifications: {'DNA': 139}
          Link IDs: {'rna3p': 138}
    Chain: "K"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1712
          Classifications: {'peptide': 205}
          Link IDs: {'PTRANS': 5, 'TRANS': 199}
          Chain breaks: 1
  Time building chain proxies: 8.98, per 1000 atoms: 0.68
  Number of scatterers: 13122
  At special positions: 0
  Unit cell: (100.98, 131.58, 118.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P     278     15.00
     O    2972      8.00
     N    2429      7.00
     C    7427      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.99
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1740

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 10 sheets defined
      65.4% alpha, 6.1% beta
      138 base pairs and 237 stacking pairs defined.
    Time for finding SS restraints: 7.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 55
      removed outlier: 3.787A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.784A  pdb=" N   VAL A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 114
    Processing helix  chain 'A' and resid 122 through 127
      removed outlier: 3.801A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   GLN A 127 " --> pdb=" O   PRO A 123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 122 through 127'
    Processing helix  chain 'B' and resid 32 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.322A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   THR B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.743A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.669A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASN C  68 " --> pdb=" O   GLU C  64 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA C  69 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.766A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.589A  pdb=" N   VAL D  41 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 67
    Processing helix  chain 'D' and resid 68 through 80
      removed outlier: 4.361A  pdb=" N   SER D  78 " --> pdb=" O   ALA D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.656A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.726A  pdb=" N   THR D 115 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   SER D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
      removed outlier: 3.678A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 78
      removed outlier: 3.808A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   LYS E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 110
      removed outlier: 3.714A  pdb=" N   LEU E  91 " --> pdb=" O   GLN E  87 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 113
      No H-bonds generated for 'chain 'E' and resid 111 through 113'
    Processing helix  chain 'E' and resid 122 through 134
      removed outlier: 3.710A  pdb=" N   ARG E 133 " --> pdb=" O   ALA E 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
      removed outlier: 3.688A  pdb=" N   GLY F  41 " --> pdb=" O   LEU F  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.565A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ASN F  64 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   TYR F  72 " --> pdb=" O   ASP F  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.675A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.707A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.936A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.580A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
      removed outlier: 3.515A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.589A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 57 through 67
    Processing helix  chain 'H' and resid 68 through 84
      removed outlier: 4.362A  pdb=" N   SER H  78 " --> pdb=" O   ALA H  74 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   HIS H  82 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.657A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.726A  pdb=" N   THR H 115 " --> pdb=" O   VAL H 111 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LYS H 116 " --> pdb=" O   SER H 112 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 4 through 16
      removed outlier: 3.528A  pdb=" N   PHE K   8 " --> pdb=" O   THR K   4 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 20 through 29
      removed outlier: 3.726A  pdb=" N   ASP K  29 " --> pdb=" O   LEU K  25 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 32 through 39
      removed outlier: 3.531A  pdb=" N   VAL K  39 " --> pdb=" O   GLN K  35 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 44 through 59
      removed outlier: 3.549A  pdb=" N   VAL K  48 " --> pdb=" O   ARG K  44 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL K  49 " --> pdb=" O   LYS K  45 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   GLN K  50 " --> pdb=" O   GLU K  46 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLU K  58 " --> pdb=" O   HIS K  54 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS K  59 " --> pdb=" O   LEU K  55 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 63 through 75
    Processing helix  chain 'K' and resid 100 through 116
      removed outlier: 3.986A  pdb=" N   PHE K 104 " --> pdb=" O   ASP K 100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 171 through 183
    Processing helix  chain 'K' and resid 197 through 210
      removed outlier: 3.983A  pdb=" N   LEU K 201 " --> pdb=" O   TYR K 197 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   GLN K 208 " --> pdb=" O   ILE K 204 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 6.798A  pdb=" N   ASN A  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.401A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86
      removed outlier: 6.926A  pdb=" N   ASN E  85 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.699A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 120 through 122
    Processing sheet with id=AB1, first strand: chain 'K' and resid 120 through 122
      removed outlier: 4.757A  pdb=" N   TYR K 151 " --> pdb=" O   SER K 164 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   TYR K 155 " --> pdb=" O   TYR K 160 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   TYR K 160 " --> pdb=" O   TYR K 155 " (cutoff:3.500A)
      removed outlier: 5.718A  pdb=" N   LEU K 193 " --> pdb=" O   VAL K  85 " (cutoff:3.500A)
      removed outlier: 8.719A  pdb=" N   GLN K  87 " --> pdb=" O   MET K 191 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   MET K 191 " --> pdb=" O   GLN K  87 " (cutoff:3.500A)
      removed outlier: 8.686A  pdb=" N   SER K  89 " --> pdb=" O   VAL K 189 " (cutoff:3.500A)
      removed outlier: 8.323A  pdb=" N   VAL K 189 " --> pdb=" O   SER K  89 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      347 hydrogen bonds
      670 hydrogen bond angles
      0 basepair planarities
      138 basepair parallelities
      237 stacking parallelities
  Total time for adding SS restraints: 4.92

  Time building geometry restraints manager: 5.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2466
        1.33 -     1.45: 4461
        1.45 -     1.57: 6426
        1.57 -     1.69: 554
        1.69 -     1.81: 29
  Bond restraints: 13936
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.497 -0.075 3.00e-02 1.11e+03 6.17e+00
  bond pdb=" C3'  DT J -61 "
       pdb=" O3'  DT J -61 "
    ideal  model  delta    sigma   weight residual
    1.422  1.489 -0.067 3.00e-02 1.11e+03 4.96e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.480 -0.058 3.00e-02 1.11e+03 3.73e+00
  bond pdb=" C3'  DA J -38 "
       pdb=" O3'  DA J -38 "
    ideal  model  delta    sigma   weight residual
    1.422  1.467 -0.045 3.00e-02 1.11e+03 2.24e+00
  bond pdb=" C3'  DC I   4 "
       pdb=" O3'  DC I   4 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.01e+00
  ... (remaining 13931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 19125
        1.81 -     3.61: 798
        3.61 -     5.42: 67
        5.42 -     7.22: 17
        7.22 -     9.03: 9
  Bond angle restraints: 20016
  Sorted by residual:
  angle pdb=" C   ARG K 169 "
        pdb=" N   ARG K 170 "
        pdb=" CA  ARG K 170 "
      ideal   model   delta    sigma   weight residual
     121.54  130.57   -9.03 1.91e+00 2.74e-01 2.23e+01
  angle pdb=" C3'  DT J -17 "
        pdb=" O3'  DT J -17 "
        pdb=" P    DT J -16 "
      ideal   model   delta    sigma   weight residual
     120.20  125.68   -5.48 1.50e+00 4.44e-01 1.34e+01
  angle pdb=" C3'  DT J -61 "
        pdb=" O3'  DT J -61 "
        pdb=" P    DA J -60 "
      ideal   model   delta    sigma   weight residual
     120.20  125.31   -5.11 1.50e+00 4.44e-01 1.16e+01
  angle pdb=" N   GLY B  99 "
        pdb=" CA  GLY B  99 "
        pdb=" C   GLY B  99 "
      ideal   model   delta    sigma   weight residual
     113.18  121.03   -7.85 2.37e+00 1.78e-01 1.10e+01
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  120.87   -7.69 2.37e+00 1.78e-01 1.05e+01
  ... (remaining 20011 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 6158
       35.97 -    71.94: 1421
       71.94 -   107.91: 33
      107.91 -   143.87: 5
      143.87 -   179.84: 3
  Dihedral angle restraints: 7620
    sinusoidal: 4930
      harmonic: 2690
  Sorted by residual:
  dihedral pdb=" CA  VAL D  66 "
           pdb=" C   VAL D  66 "
           pdb=" N   ASN D  67 "
           pdb=" CA  ASN D  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.03   26.97     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  VAL H  66 "
           pdb=" C   VAL H  66 "
           pdb=" N   ASN H  67 "
           pdb=" CA  ASN H  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.05   26.95     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  TYR B  98 "
           pdb=" C   TYR B  98 "
           pdb=" N   GLY B  99 "
           pdb=" CA  GLY B  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.10  -22.90     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 7617 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1965
       0.066 -    0.132: 269
       0.132 -    0.198: 34
       0.198 -    0.264: 0
       0.264 -    0.330: 2
  Chirality restraints: 2270
  Sorted by residual:
  chirality pdb=" CB  VAL H  66 "
            pdb=" CA  VAL H  66 "
            pdb=" CG1 VAL H  66 "
            pdb=" CG2 VAL H  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" CB  VAL D  66 "
            pdb=" CA  VAL D  66 "
            pdb=" CG1 VAL D  66 "
            pdb=" CG2 VAL D  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" P    DT J -16 "
            pdb=" OP1  DT J -16 "
            pdb=" OP2  DT J -16 "
            pdb=" O5'  DT J -16 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.54   -0.19 2.00e-01 2.50e+01 9.08e-01
  ... (remaining 2267 not shown)

  Planarity restraints: 1559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  63 "   -0.017 2.00e-02 2.50e+03   3.43e-02 1.17e+01
        pdb=" C   GLU B  63 "    0.059 2.00e-02 2.50e+03
        pdb=" O   GLU B  63 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ASN B  64 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  31 "    0.051 5.00e-02 4.00e+02   7.67e-02 9.41e+00
        pdb=" N   PRO B  32 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  57 "   -0.014 2.00e-02 2.50e+03   2.79e-02 7.81e+00
        pdb=" C   VAL F  57 "    0.048 2.00e-02 2.50e+03
        pdb=" O   VAL F  57 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU F  58 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1556 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 403
        2.67 -     3.22: 10868
        3.22 -     3.78: 23903
        3.78 -     4.34: 29972
        4.34 -     4.90: 42476
  Nonbonded interactions: 107622
  Sorted by model distance:
  nonbonded pdb=" O   TYR B  51 "
            pdb=" NH1 ARG B  55 "
     model   vdw
     2.107 3.120
  nonbonded pdb=" NH1 ARG F  39 "
            pdb=" O   LYS F  44 "
     model   vdw
     2.145 3.120
  nonbonded pdb=" OD2 ASP K  70 "
            pdb=" OH  TYR K 151 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OH  TYR H  42 "
            pdb=" NZ  LYS H  46 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OH  TYR D  42 "
            pdb=" NZ  LYS D  46 "
     model   vdw
     2.190 3.120
  ... (remaining 107617 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 46 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 15 through 112)
  selection = (chain 'G' and resid 15 through 112)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:             0.040
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     44.890
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
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   0.075  13936  Z= 0.260
  Angle     :  0.810   9.028  20016  Z= 0.473
  Chirality :  0.047   0.330   2270
  Planarity :  0.006   0.077   1559
  Dihedral  : 27.862 179.844   5880
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.19 (0.20), residues: 905
  helix: -2.61 (0.14), residues: 605
  sheet: -1.52 (0.80), residues: 38
  loop : -2.86 (0.32), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP K  28 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.026   0.002   PHE F 100 
 TYR   0.014   0.002   TYR F  88 
 ARG   0.006   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14517 (  743)
  hydrogen bonds       : angle       5.89985 ( 1855)
  covalent geometry    : bond        0.00580 (13936)
  covalent geometry    : angle       0.80981 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 385
  time to evaluate  : 0.978 
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   87 GLN cc_start: 0.8295 (mt0) cc_final: 0.8001 (mt0)
REVERT: A  133 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7795 (mtp85)
REVERT: B   44 LYS cc_start: 0.8028 (mttt) cc_final: 0.7744 (mttt)
REVERT: B   88 TYR cc_start: 0.8530 (m-10) cc_final: 0.8254 (m-10)
REVERT: C   23 LEU cc_start: 0.9074 (mt) cc_final: 0.8688 (mp)
REVERT: C   79 ILE cc_start: 0.9316 (pt) cc_final: 0.9053 (mt)
REVERT: D  105 GLU cc_start: 0.7384 (tp30) cc_final: 0.7167 (tp30)
REVERT: E   58 THR cc_start: 0.9151 (p) cc_final: 0.8545 (t)
REVERT: G   42 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7056 (mtp85)
REVERT: G  111 ILE cc_start: 0.8253 (mt) cc_final: 0.7882 (mt)
REVERT: H   36 SER cc_start: 0.8774 (t) cc_final: 0.8458 (t)
REVERT: H   52 THR cc_start: 0.9145 (m) cc_final: 0.8926 (m)
REVERT: H  101 LEU cc_start: 0.8376 (mm) cc_final: 0.7948 (mt)
REVERT: K    5 VAL cc_start: 0.8963 (m) cc_final: 0.8655 (t)
REVERT: K   70 ASP cc_start: 0.8059 (t70) cc_final: 0.7579 (t0)
REVERT: K  106 ASN cc_start: 0.9100 (m110) cc_final: 0.8612 (m-40)
REVERT: K  135 ILE cc_start: 0.9027 (mp) cc_final: 0.8715 (tt)
REVERT: K  150 THR cc_start: 0.9140 (m) cc_final: 0.8939 (m)
REVERT: K  158 THR cc_start: 0.7579 (p) cc_final: 0.7281 (p)
REVERT: K  191 MET cc_start: 0.6136 (mtt) cc_final: 0.5671 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 385
  average time/residue: 0.3664
  time to fit residues: 182.7526
Evaluate side-chains
  279 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 34 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
C  31 HIS
C  68 ASN
C  89 ASN
C 110 ASN
G  31 HIS
G  38 ASN
G  73 ASN
G  94 ASN
H  47 GLN
H  67 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  75 GLN
K 106 ASN
K 145 ASN
K 146 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.126249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.088608 restraints weight = 26493.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.091004 restraints weight = 15631.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.092572 restraints weight = 11351.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13936  Z= 0.214
  Angle     :  0.664   7.335  20016  Z= 0.382
  Chirality :  0.038   0.185   2270
  Planarity :  0.005   0.060   1559
  Dihedral  : 31.737 178.530   4054
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 16.33 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.25), residues: 905
  helix: -0.63 (0.19), residues: 609
  sheet: -0.69 (0.77), residues: 38
  loop : -2.65 (0.33), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP K  28 
 HIS   0.006   0.001   HIS E  59 
 PHE   0.013   0.002   PHE K 108 
 TYR   0.014   0.002   TYR K 151 
 ARG   0.006   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06289 (  743)
  hydrogen bonds       : angle       3.63429 ( 1855)
  covalent geometry    : bond        0.00474 (13936)
  covalent geometry    : angle       0.66352 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 318
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8309 (ttmm)
REVERT: A  133 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8054 (mtp85)
REVERT: B   53 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7887 (tm-30)
REVERT: B   75 HIS cc_start: 0.8966 (t-90) cc_final: 0.8764 (t-170)
REVERT: B   84 MET cc_start: 0.8084 (mmm) cc_final: 0.7691 (mmm)
REVERT: B   88 TYR cc_start: 0.8763 (m-10) cc_final: 0.8386 (m-80)
REVERT: C   35 ARG cc_start: 0.8336 (mtm110) cc_final: 0.8089 (mtm-85)
REVERT: C   61 GLU cc_start: 0.8010 (tp30) cc_final: 0.7804 (tp30)
REVERT: D   43 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8421 (ttpt)
REVERT: D   51 ASP cc_start: 0.7966 (p0) cc_final: 0.7753 (p0)
REVERT: F   29 ILE cc_start: 0.8927 (mm) cc_final: 0.8669 (mp)
REVERT: G   39 TYR cc_start: 0.8972 (m-10) cc_final: 0.8574 (m-80)
REVERT: H   86 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8308 (mmm-85)
REVERT: K    5 VAL cc_start: 0.9055 (m) cc_final: 0.8697 (t)
REVERT: K    7 GLU cc_start: 0.7813 (mp0) cc_final: 0.7534 (mp0)
REVERT: K   70 ASP cc_start: 0.8763 (t70) cc_final: 0.8373 (t0)
REVERT: K   86 PHE cc_start: 0.8653 (m-80) cc_final: 0.8324 (m-80)
REVERT: K  106 ASN cc_start: 0.9434 (m-40) cc_final: 0.8993 (m110)
REVERT: K  108 PHE cc_start: 0.8746 (t80) cc_final: 0.8436 (t80)
REVERT: K  135 ILE cc_start: 0.9075 (mp) cc_final: 0.8864 (mp)
REVERT: K  152 VAL cc_start: 0.9628 (t) cc_final: 0.9329 (m)
REVERT: K  162 PHE cc_start: 0.8464 (m-10) cc_final: 0.8261 (m-10)
REVERT: K  170 ARG cc_start: 0.8508 (ptm160) cc_final: 0.7730 (ttm170)
REVERT: K  191 MET cc_start: 0.6127 (mtt) cc_final: 0.5297 (tmm)
  outliers start: 24
  outliers final: 14
  residues processed: 326
  average time/residue: 0.3337
  time to fit residues: 143.8513
Evaluate side-chains
  292 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 278
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   85 ASP
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   56 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 108 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 32 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
F  64 ASN
G  38 ASN
H  67 ASN
H  82 HIS
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  77 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.127481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.090507 restraints weight = 26779.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.092882 restraints weight = 15318.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.093903 restraints weight = 10781.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13936  Z= 0.168
  Angle     :  0.614   9.302  20016  Z= 0.355
  Chirality :  0.036   0.128   2270
  Planarity :  0.004   0.043   1559
  Dihedral  : 31.505 179.522   4054
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.54 %
    Favored  : 76.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.27), residues: 905
  helix:  0.27 (0.21), residues: 606
  sheet: -0.21 (0.77), residues: 38
  loop : -2.31 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K  28 
 HIS   0.003   0.001   HIS H  82 
 PHE   0.028   0.001   PHE K 108 
 TYR   0.018   0.002   TYR H 121 
 ARG   0.007   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05764 (  743)
  hydrogen bonds       : angle       3.14920 ( 1855)
  covalent geometry    : bond        0.00369 (13936)
  covalent geometry    : angle       0.61368 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 301
  time to evaluate  : 1.064 
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  133 ARG cc_start: 0.8320 (ttm170) cc_final: 0.8067 (mtp85)
REVERT: B   53 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: B   75 HIS cc_start: 0.8957 (t-90) cc_final: 0.8635 (t-170)
REVERT: B   84 MET cc_start: 0.8029 (mmm) cc_final: 0.7755 (mmm)
REVERT: B   88 TYR cc_start: 0.8793 (m-10) cc_final: 0.8402 (m-80)
REVERT: D   43 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8279 (ttpt)
REVERT: E  127 GLN cc_start: 0.8109 (mt0) cc_final: 0.7798 (mm-40)
REVERT: E  131 ARG cc_start: 0.9113 (tpp80) cc_final: 0.8900 (tpp80)
REVERT: G   39 TYR cc_start: 0.8980 (m-10) cc_final: 0.8510 (m-80)
REVERT: G   41 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6542 (tm-30)
REVERT: G   61 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8608 (tm-30)
REVERT: G  111 ILE cc_start: 0.8062 (mt) cc_final: 0.7850 (mt)
REVERT: H   86 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8277 (mmm-85)
REVERT: H  101 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7812 (mt)
REVERT: K    3 GLU cc_start: 0.8091 (tp30) cc_final: 0.7889 (tp30)
REVERT: K    5 VAL cc_start: 0.8881 (m) cc_final: 0.8519 (t)
REVERT: K   70 ASP cc_start: 0.8695 (t70) cc_final: 0.8352 (t0)
REVERT: K   86 PHE cc_start: 0.8585 (m-80) cc_final: 0.8277 (m-80)
REVERT: K  123 PHE cc_start: 0.7968 (m-80) cc_final: 0.7715 (m-80)
REVERT: K  152 VAL cc_start: 0.9582 (t) cc_final: 0.9254 (m)
REVERT: K  170 ARG cc_start: 0.8483 (ptm160) cc_final: 0.8192 (ttp-170)
REVERT: K  191 MET cc_start: 0.6053 (mtt) cc_final: 0.5124 (tmm)
  outliers start: 23
  outliers final: 12
  residues processed: 308
  average time/residue: 0.3326
  time to fit residues: 135.2538
Evaluate side-chains
  283 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 270
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 43 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 11 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
A 115 HIS
E  85 ASN
G  38 ASN
H  82 HIS
K 113 GLN
K 118 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.126724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.088458 restraints weight = 26496.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.090815 restraints weight = 15808.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.092313 restraints weight = 11571.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
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      :  0.004   0.043  13936  Z= 0.189
  Angle     :  0.622   7.892  20016  Z= 0.357
  Chirality :  0.037   0.142   2270
  Planarity :  0.004   0.049   1559
  Dihedral  : 31.442 178.651   4054
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 21.94 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.28), residues: 905
  helix:  0.68 (0.21), residues: 606
  sheet:  0.28 (0.82), residues: 38
  loop : -2.04 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K  28 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.013   0.001   PHE K 104 
 TYR   0.025   0.002   TYR H  83 
 ARG   0.008   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05801 (  743)
  hydrogen bonds       : angle       3.08718 ( 1855)
  covalent geometry    : bond        0.00418 (13936)
  covalent geometry    : angle       0.62233 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 285
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 ARG cc_start: 0.8326 (ttm170) cc_final: 0.8100 (mtp85)
REVERT: B   53 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7575 (tm-30)
REVERT: B   84 MET cc_start: 0.8022 (mmm) cc_final: 0.7750 (mmm)
REVERT: B   88 TYR cc_start: 0.8771 (m-10) cc_final: 0.8339 (m-80)
REVERT: C   94 ASN cc_start: 0.9184 (t0) cc_final: 0.8917 (t0)
REVERT: D   43 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8358 (ttpt)
REVERT: G   39 TYR cc_start: 0.9097 (m-10) cc_final: 0.8585 (m-80)
REVERT: G   41 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6656 (tm-30)
REVERT: G   84 GLN cc_start: 0.9113 (tp40) cc_final: 0.8257 (tt0)
REVERT: H  101 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7846 (mt)
REVERT: K    5 VAL cc_start: 0.8834 (m) cc_final: 0.8499 (t)
REVERT: K   70 ASP cc_start: 0.8768 (t70) cc_final: 0.8283 (t0)
REVERT: K   86 PHE cc_start: 0.8614 (m-80) cc_final: 0.8366 (m-80)
REVERT: K  123 PHE cc_start: 0.7980 (m-80) cc_final: 0.7706 (m-80)
REVERT: K  152 VAL cc_start: 0.9620 (t) cc_final: 0.9312 (m)
REVERT: K  170 ARG cc_start: 0.8482 (ptm160) cc_final: 0.8231 (ttp-170)
REVERT: K  191 MET cc_start: 0.6128 (mtt) cc_final: 0.5080 (tmm)
REVERT: K  196 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7119 (ttm170)
  outliers start: 37
  outliers final: 27
  residues processed: 303
  average time/residue: 0.2967
  time to fit residues: 121.6330
Evaluate side-chains
  299 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 271
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   27 VAL
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   44 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue  156 SER
Chi-restraints excluded: chain K residue  163 THR
Chi-restraints excluded: chain K residue  175 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 68 optimal weight:   30.0000
   chunk 9 optimal weight:    0.7980
   chunk 49 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0870
   chunk 98 optimal weight:    8.9990
   chunk 109 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    3.3764

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

Flipped N/Q/H residues before XYZ refinement:
E  85 ASN
H  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.126771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.089967 restraints weight = 26556.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.092305 restraints weight = 14927.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.093306 restraints weight = 10311.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13936  Z= 0.182
  Angle     :  0.616   6.054  20016  Z= 0.356
  Chirality :  0.036   0.160   2270
  Planarity :  0.004   0.047   1559
  Dihedral  : 31.360 178.688   4054
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 20.54 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.28), residues: 905
  helix:  0.92 (0.21), residues: 607
  sheet:  0.43 (0.83), residues: 38
  loop : -1.89 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  28 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.013   0.001   PHE K 206 
 TYR   0.038   0.002   TYR H  83 
 ARG   0.007   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05726 (  743)
  hydrogen bonds       : angle       2.98706 ( 1855)
  covalent geometry    : bond        0.00404 (13936)
  covalent geometry    : angle       0.61650 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 295
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8496 (mpp80) cc_final: 0.7957 (mtm-85)
REVERT: A  133 ARG cc_start: 0.8345 (ttm170) cc_final: 0.8104 (mtp85)
REVERT: B   53 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7549 (tm-30)
REVERT: B   84 MET cc_start: 0.7978 (mmm) cc_final: 0.7756 (mmm)
REVERT: B   88 TYR cc_start: 0.8773 (m-10) cc_final: 0.8311 (m-80)
REVERT: C   41 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8145 (mp0)
REVERT: C   61 GLU cc_start: 0.8054 (tp30) cc_final: 0.7137 (tp30)
REVERT: C   94 ASN cc_start: 0.9194 (t0) cc_final: 0.8965 (t0)
REVERT: D   43 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8359 (ttpt)
REVERT: F   84 MET cc_start: 0.7992 (tpp) cc_final: 0.7743 (tpp)
REVERT: G   39 TYR cc_start: 0.9008 (m-80) cc_final: 0.8541 (m-80)
REVERT: H   91 SER cc_start: 0.8851 (p) cc_final: 0.8398 (t)
REVERT: H  101 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7790 (mt)
REVERT: K    5 VAL cc_start: 0.8784 (m) cc_final: 0.8498 (t)
REVERT: K   33 GLU cc_start: 0.8292 (mp0) cc_final: 0.7695 (mm-30)
REVERT: K   37 GLN cc_start: 0.8159 (mt0) cc_final: 0.7561 (mp10)
REVERT: K   70 ASP cc_start: 0.8741 (t70) cc_final: 0.8364 (t0)
REVERT: K   85 VAL cc_start: 0.6997 (p) cc_final: 0.6757 (p)
REVERT: K   86 PHE cc_start: 0.8549 (m-80) cc_final: 0.8326 (m-80)
REVERT: K   88 MET cc_start: 0.3325 (mmm) cc_final: 0.2791 (mmm)
REVERT: K  122 SER cc_start: 0.8217 (m) cc_final: 0.7863 (p)
REVERT: K  123 PHE cc_start: 0.7964 (m-80) cc_final: 0.7758 (m-80)
REVERT: K  152 VAL cc_start: 0.9598 (t) cc_final: 0.9298 (m)
REVERT: K  170 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7777 (ttm170)
REVERT: K  185 HIS cc_start: 0.8553 (m90) cc_final: 0.7866 (m-70)
REVERT: K  191 MET cc_start: 0.6214 (mtt) cc_final: 0.5266 (tmm)
REVERT: K  196 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.7079 (ttm170)
  outliers start: 46
  outliers final: 34
  residues processed: 313
  average time/residue: 0.3364
  time to fit residues: 140.6167
Evaluate side-chains
  311 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 275
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   36 SER
Chi-restraints excluded: chain H residue   44 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   63 ILE
Chi-restraints excluded: chain K residue  163 THR
Chi-restraints excluded: chain K residue  170 ARG
Chi-restraints excluded: chain K residue  175 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 108 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0060
   chunk 39 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0170
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    9.9990
   chunk 93 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.2040

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

Flipped N/Q/H residues before XYZ refinement:
H  82 HIS
K  87 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.130141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.092577 restraints weight = 27028.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.095017 restraints weight = 15543.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.096599 restraints weight = 11186.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13936  Z= 0.146
  Angle     :  0.593   8.186  20016  Z= 0.342
  Chirality :  0.035   0.179   2270
  Planarity :  0.004   0.038   1559
  Dihedral  : 31.109 179.546   4054
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.62 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.29), residues: 905
  helix:  1.15 (0.21), residues: 609
  sheet:  0.93 (0.84), residues: 38
  loop : -1.76 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K 132 
 HIS   0.008   0.001   HIS H  82 
 PHE   0.011   0.001   PHE K 104 
 TYR   0.014   0.002   TYR C  50 
 ARG   0.008   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05405 (  743)
  hydrogen bonds       : angle       2.78122 ( 1855)
  covalent geometry    : bond        0.00317 (13936)
  covalent geometry    : angle       0.59307 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 292
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8446 (mpp80) cc_final: 0.7932 (mtm-85)
REVERT: A  114 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9249 (mm)
REVERT: A  133 ARG cc_start: 0.8309 (ttm170) cc_final: 0.8036 (mtm110)
REVERT: B   53 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: B   88 TYR cc_start: 0.8756 (m-10) cc_final: 0.8372 (m-80)
REVERT: C   38 ASN cc_start: 0.8725 (t0) cc_final: 0.8465 (t0)
REVERT: C   61 GLU cc_start: 0.7874 (tp30) cc_final: 0.7517 (tp30)
REVERT: C   94 ASN cc_start: 0.9154 (t0) cc_final: 0.8903 (t0)
REVERT: D   43 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8361 (ttpt)
REVERT: E   70 LEU cc_start: 0.9015 (tp) cc_final: 0.8806 (tt)
REVERT: E  127 GLN cc_start: 0.8305 (mt0) cc_final: 0.8017 (mm-40)
REVERT: G   39 TYR cc_start: 0.8979 (m-80) cc_final: 0.8420 (m-80)
REVERT: G   84 GLN cc_start: 0.9082 (tp40) cc_final: 0.8292 (tt0)
REVERT: H   83 TYR cc_start: 0.6947 (m-80) cc_final: 0.6424 (m-80)
REVERT: H   86 ARG cc_start: 0.8792 (tpp80) cc_final: 0.8461 (tpp80)
REVERT: H  101 LEU cc_start: 0.8230 (mm) cc_final: 0.7829 (mt)
REVERT: K    5 VAL cc_start: 0.8580 (m) cc_final: 0.8305 (t)
REVERT: K   70 ASP cc_start: 0.8770 (t70) cc_final: 0.8390 (t0)
REVERT: K   86 PHE cc_start: 0.8630 (m-80) cc_final: 0.8428 (m-80)
REVERT: K   88 MET cc_start: 0.3000 (mmm) cc_final: 0.2646 (mmm)
REVERT: K  106 ASN cc_start: 0.9385 (m-40) cc_final: 0.8855 (m110)
REVERT: K  111 ILE cc_start: 0.8486 (mm) cc_final: 0.6744 (mm)
REVERT: K  122 SER cc_start: 0.8217 (m) cc_final: 0.7876 (p)
REVERT: K  152 VAL cc_start: 0.9633 (t) cc_final: 0.9365 (m)
REVERT: K  160 TYR cc_start: 0.8157 (m-80) cc_final: 0.7692 (m-80)
REVERT: K  170 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8252 (ttp-170)
REVERT: K  185 HIS cc_start: 0.8653 (m90) cc_final: 0.7888 (m-70)
REVERT: K  191 MET cc_start: 0.5950 (mtt) cc_final: 0.5063 (tmm)
  outliers start: 21
  outliers final: 11
  residues processed: 300
  average time/residue: 0.3171
  time to fit residues: 127.6062
Evaluate side-chains
  286 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 273
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain K residue  163 THR
Chi-restraints excluded: chain K residue  170 ARG
Chi-restraints excluded: chain K residue  175 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:   30.0000
   chunk 22 optimal weight:    7.9990
   chunk 24 optimal weight:    0.8980
   chunk 103 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0870
   chunk 44 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 35 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
A  85 ASN
E  85 ASN
H  82 HIS
K  75 GLN
K  87 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.130464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.092816 restraints weight = 26738.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.095253 restraints weight = 15394.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.096806 restraints weight = 11093.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13936  Z= 0.150
  Angle     :  0.593   7.502  20016  Z= 0.343
  Chirality :  0.035   0.163   2270
  Planarity :  0.003   0.030   1559
  Dihedral  : 31.049 178.672   4054
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.38 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.29), residues: 905
  helix:  1.24 (0.21), residues: 611
  sheet:  0.86 (0.88), residues: 38
  loop : -1.64 (0.39), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  83 
 HIS   0.006   0.001   HIS H  82 
 PHE   0.010   0.001   PHE K 162 
 TYR   0.019   0.002   TYR K 154 
 ARG   0.008   0.001   ARG K 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05379 (  743)
  hydrogen bonds       : angle       2.78145 ( 1855)
  covalent geometry    : bond        0.00327 (13936)
  covalent geometry    : angle       0.59336 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 282
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8487 (mpp80) cc_final: 0.7962 (mtm-85)
REVERT: A  114 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9230 (mm)
REVERT: B   88 TYR cc_start: 0.8655 (m-10) cc_final: 0.8121 (m-10)
REVERT: C   34 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8686 (tt)
REVERT: C   61 GLU cc_start: 0.7830 (tp30) cc_final: 0.7572 (tp30)
REVERT: C   94 ASN cc_start: 0.9159 (t0) cc_final: 0.8880 (t0)
REVERT: D   43 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8407 (ttpt)
REVERT: E   70 LEU cc_start: 0.8998 (tp) cc_final: 0.8792 (tt)
REVERT: E  127 GLN cc_start: 0.8312 (mt0) cc_final: 0.8014 (mm-40)
REVERT: G   39 TYR cc_start: 0.9041 (m-80) cc_final: 0.8557 (m-80)
REVERT: G   84 GLN cc_start: 0.9080 (tp40) cc_final: 0.8286 (tt0)
REVERT: H   62 MET cc_start: 0.9049 (mmm) cc_final: 0.8720 (tpp)
REVERT: H  115 THR cc_start: 0.8734 (m) cc_final: 0.8394 (p)
REVERT: K   70 ASP cc_start: 0.8749 (t70) cc_final: 0.8388 (t0)
REVERT: K   88 MET cc_start: 0.3156 (mmm) cc_final: 0.2921 (mmm)
REVERT: K  106 ASN cc_start: 0.9388 (m-40) cc_final: 0.8856 (m110)
REVERT: K  111 ILE cc_start: 0.8390 (mm) cc_final: 0.7853 (mt)
REVERT: K  122 SER cc_start: 0.8077 (m) cc_final: 0.7709 (p)
REVERT: K  123 PHE cc_start: 0.7848 (m-80) cc_final: 0.7556 (m-80)
REVERT: K  151 TYR cc_start: 0.9068 (m-10) cc_final: 0.8861 (m-10)
REVERT: K  160 TYR cc_start: 0.8270 (m-80) cc_final: 0.7748 (m-80)
REVERT: K  170 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8231 (ttp-170)
REVERT: K  185 HIS cc_start: 0.8678 (m90) cc_final: 0.7920 (m-70)
REVERT: K  191 MET cc_start: 0.6118 (mtt) cc_final: 0.5227 (tpt)
  outliers start: 23
  outliers final: 17
  residues processed: 293
  average time/residue: 0.3086
  time to fit residues: 121.4457
Evaluate side-chains
  292 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 272
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain K residue  163 THR
Chi-restraints excluded: chain K residue  170 ARG
Chi-restraints excluded: chain K residue  175 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 17 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 ASN
H  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.125577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.087022 restraints weight = 26935.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.089307 restraints weight = 15988.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.090758 restraints weight = 11734.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  13936  Z= 0.238
  Angle     :  0.670   6.883  20016  Z= 0.380
  Chirality :  0.039   0.156   2270
  Planarity :  0.004   0.035   1559
  Dihedral  : 31.309 176.756   4054
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 24.62 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.28), residues: 905
  helix:  1.04 (0.21), residues: 611
  sheet:  1.06 (0.85), residues: 38
  loop : -1.82 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  28 
 HIS   0.016   0.001   HIS H  82 
 PHE   0.017   0.002   PHE A  67 
 TYR   0.036   0.002   TYR H  83 
 ARG   0.007   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06212 (  743)
  hydrogen bonds       : angle       3.19384 ( 1855)
  covalent geometry    : bond        0.00534 (13936)
  covalent geometry    : angle       0.66981 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 269
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8711 (m-10) cc_final: 0.8074 (m-10)
REVERT: C   92 GLU cc_start: 0.7846 (pm20) cc_final: 0.7497 (pm20)
REVERT: C   94 ASN cc_start: 0.9324 (t0) cc_final: 0.9035 (t0)
REVERT: D   43 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8305 (ttpt)
REVERT: G   77 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7379 (mtt90)
REVERT: G   84 GLN cc_start: 0.9157 (tp40) cc_final: 0.8410 (tt0)
REVERT: H   62 MET cc_start: 0.9067 (mmm) cc_final: 0.8838 (tpp)
REVERT: H   79 ARG cc_start: 0.8302 (ttm170) cc_final: 0.8049 (mtm110)
REVERT: H   86 ARG cc_start: 0.8979 (tpp80) cc_final: 0.8738 (tpp80)
REVERT: H  101 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7906 (mt)
REVERT: K   70 ASP cc_start: 0.8803 (t70) cc_final: 0.8379 (t0)
REVERT: K   88 MET cc_start: 0.3466 (mmm) cc_final: 0.3143 (mmm)
REVERT: K  106 ASN cc_start: 0.9401 (m-40) cc_final: 0.8860 (m110)
REVERT: K  122 SER cc_start: 0.8052 (m) cc_final: 0.7785 (p)
REVERT: K  123 PHE cc_start: 0.7903 (m-80) cc_final: 0.7647 (m-80)
REVERT: K  152 VAL cc_start: 0.9629 (t) cc_final: 0.9382 (m)
REVERT: K  160 TYR cc_start: 0.8355 (m-80) cc_final: 0.7823 (m-80)
REVERT: K  170 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8045 (ttm170)
REVERT: K  185 HIS cc_start: 0.8714 (m90) cc_final: 0.7811 (m-70)
REVERT: K  191 MET cc_start: 0.6280 (mtt) cc_final: 0.5176 (tpt)
REVERT: K  196 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.7066 (ptm160)
  outliers start: 37
  outliers final: 31
  residues processed: 286
  average time/residue: 0.3188
  time to fit residues: 121.5289
Evaluate side-chains
  290 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 257
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   68 ASP
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   78 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue  158 THR
Chi-restraints excluded: chain K residue  163 THR
Chi-restraints excluded: chain K residue  170 ARG
Chi-restraints excluded: chain K residue  175 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 87 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 96 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
E  85 ASN
E 127 GLN
H  82 HIS
** H  84 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 = 0.3817 r_free = 0.3817 target = 0.127503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.089239 restraints weight = 26575.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.091623 restraints weight = 15556.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.093136 restraints weight = 11299.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13936  Z= 0.175
  Angle     :  0.633   9.603  20016  Z= 0.362
  Chirality :  0.036   0.162   2270
  Planarity :  0.004   0.034   1559
  Dihedral  : 31.176 178.257   4054
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 25.26 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.29), residues: 905
  helix:  1.17 (0.21), residues: 605
  sheet:  1.24 (0.89), residues: 38
  loop : -1.46 (0.39), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  47 
 HIS   0.007   0.001   HIS H  82 
 PHE   0.013   0.001   PHE K 162 
 TYR   0.023   0.002   TYR K 154 
 ARG   0.011   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05649 (  743)
  hydrogen bonds       : angle       2.95605 ( 1855)
  covalent geometry    : bond        0.00392 (13936)
  covalent geometry    : angle       0.63321 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 270
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8502 (mpp80) cc_final: 0.8038 (mtm-85)
REVERT: B   84 MET cc_start: 0.8093 (tpp) cc_final: 0.7809 (mmm)
REVERT: B   88 TYR cc_start: 0.8806 (m-10) cc_final: 0.8410 (m-80)
REVERT: C   23 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8581 (mp)
REVERT: C   94 ASN cc_start: 0.9288 (t0) cc_final: 0.9007 (t0)
REVERT: D   43 LYS cc_start: 0.8713 (ttpt) cc_final: 0.8322 (ttpt)
REVERT: E  127 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7993 (mm-40)
REVERT: F   40 ARG cc_start: 0.8938 (ttm170) cc_final: 0.8730 (ttm170)
REVERT: G   84 GLN cc_start: 0.9113 (tp40) cc_final: 0.8261 (tt0)
REVERT: H   68 ASP cc_start: 0.8908 (t0) cc_final: 0.8370 (t0)
REVERT: H   86 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8527 (tpp80)
REVERT: H   91 SER cc_start: 0.8844 (p) cc_final: 0.8306 (t)
REVERT: H  101 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7852 (mt)
REVERT: K   70 ASP cc_start: 0.8793 (t70) cc_final: 0.8375 (t0)
REVERT: K   88 MET cc_start: 0.3334 (mmm) cc_final: 0.3075 (mmm)
REVERT: K  106 ASN cc_start: 0.9386 (m-40) cc_final: 0.8828 (m110)
REVERT: K  122 SER cc_start: 0.8023 (m) cc_final: 0.7721 (p)
REVERT: K  123 PHE cc_start: 0.7894 (m-80) cc_final: 0.7637 (m-80)
REVERT: K  152 VAL cc_start: 0.9641 (t) cc_final: 0.9395 (m)
REVERT: K  160 TYR cc_start: 0.8423 (m-80) cc_final: 0.7829 (m-80)
REVERT: K  170 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7658 (ttm170)
REVERT: K  185 HIS cc_start: 0.8651 (m90) cc_final: 0.7797 (m-70)
REVERT: K  191 MET cc_start: 0.6154 (mtt) cc_final: 0.5009 (tpt)
  outliers start: 31
  outliers final: 25
  residues processed: 286
  average time/residue: 0.3248
  time to fit residues: 124.9701
Evaluate side-chains
  291 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 262
  time to evaluate  : 1.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  127 GLN
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue  163 THR
Chi-restraints excluded: chain K residue  170 ARG
Chi-restraints excluded: chain K residue  175 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 80 optimal weight:   20.0000
   chunk 88 optimal weight:   10.0000
   overall best weight:    5.3992

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

Flipped N/Q/H residues before XYZ refinement:
E  85 ASN
E 127 GLN
H  82 HIS
K 185 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.125403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.086844 restraints weight = 26620.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.089091 restraints weight = 15914.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.090552 restraints weight = 11744.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13936  Z= 0.239
  Angle     :  0.693   9.620  20016  Z= 0.390
  Chirality :  0.038   0.184   2270
  Planarity :  0.005   0.064   1559
  Dihedral  : 31.284 177.655   4054
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 25.38 %
    Favored  : 69.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.29), residues: 905
  helix:  0.99 (0.21), residues: 620
  sheet:  1.13 (0.89), residues: 38
  loop : -1.60 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP K  28 
 HIS   0.008   0.001   HIS H  82 
 PHE   0.015   0.001   PHE A  67 
 TYR   0.018   0.002   TYR G  39 
 ARG   0.013   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06134 (  743)
  hydrogen bonds       : angle       3.21543 ( 1855)
  covalent geometry    : bond        0.00539 (13936)
  covalent geometry    : angle       0.69259 (20016)

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

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

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1810 Ramachandran restraints generated.
    905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 263
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ARG cc_start: 0.8495 (mpp80) cc_final: 0.7944 (mtm-85)
REVERT: B   88 TYR cc_start: 0.8784 (m-10) cc_final: 0.8145 (m-10)
REVERT: C   23 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8552 (mp)
REVERT: C   94 ASN cc_start: 0.9345 (t0) cc_final: 0.9036 (t0)
REVERT: D   43 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8349 (ttpt)
REVERT: D  109 HIS cc_start: 0.8180 (m170) cc_final: 0.7937 (m170)
REVERT: E  127 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8015 (mm-40)
REVERT: F   40 ARG cc_start: 0.8960 (ttm170) cc_final: 0.8691 (ttm170)
REVERT: G   84 GLN cc_start: 0.9118 (tp40) cc_final: 0.8269 (tt0)
REVERT: H   86 ARG cc_start: 0.8902 (tpp80) cc_final: 0.8637 (tpp80)
REVERT: H   91 SER cc_start: 0.8941 (p) cc_final: 0.8592 (t)
REVERT: H  101 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7959 (mt)
REVERT: K   70 ASP cc_start: 0.8814 (t70) cc_final: 0.8341 (t0)
REVERT: K   88 MET cc_start: 0.3312 (mmm) cc_final: 0.3093 (mmm)
REVERT: K  106 ASN cc_start: 0.9322 (m-40) cc_final: 0.8798 (m110)
REVERT: K  122 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7801 (p)
REVERT: K  123 PHE cc_start: 0.7900 (m-80) cc_final: 0.7613 (m-80)
REVERT: K  152 VAL cc_start: 0.9636 (t) cc_final: 0.9379 (m)
REVERT: K  160 TYR cc_start: 0.8484 (m-80) cc_final: 0.7908 (m-80)
REVERT: K  170 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8111 (ttm170)
REVERT: K  185 HIS cc_start: 0.8672 (m-70) cc_final: 0.7815 (m-70)
REVERT: K  191 MET cc_start: 0.6217 (mtt) cc_final: 0.5084 (tpt)
  outliers start: 38
  outliers final: 31
  residues processed: 279
  average time/residue: 0.4138
  time to fit residues: 160.4773
Evaluate side-chains
  288 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 252
  time to evaluate  : 1.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain B residue   26 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   55 LEU
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  113 THR
Chi-restraints excluded: chain E residue  119 VAL
Chi-restraints excluded: chain E residue  127 GLN
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   58 LEU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   44 VAL
Chi-restraints excluded: chain H residue   66 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain K residue   63 ILE
Chi-restraints excluded: chain K residue  122 SER
Chi-restraints excluded: chain K residue  158 THR
Chi-restraints excluded: chain K residue  163 THR
Chi-restraints excluded: chain K residue  170 ARG
Chi-restraints excluded: chain K residue  175 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 108 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
E  85 ASN
E 127 GLN
H  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.126861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.088344 restraints weight = 26758.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.090665 restraints weight = 15808.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.092173 restraints weight = 11570.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13936  Z= 0.187
  Angle     :  0.659   9.807  20016  Z= 0.375
  Chirality :  0.037   0.164   2270
  Planarity :  0.004   0.060   1559
  Dihedral  : 31.184 178.150   4054
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 25.89 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.29), residues: 905
  helix:  1.17 (0.21), residues: 614
  sheet:  1.20 (0.90), residues: 38
  loop : -1.45 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  28 
 HIS   0.010   0.001   HIS H  82 
 PHE   0.014   0.001   PHE K 162 
 TYR   0.023   0.002   TYR K 154 
 ARG   0.013   0.001   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05777 (  743)
  hydrogen bonds       : angle       3.03321 ( 1855)
  covalent geometry    : bond        0.00420 (13936)
  covalent geometry    : angle       0.65922 (20016)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4500.49 seconds
wall clock time: 80 minutes 37.79 seconds (4837.79 seconds total)