Starting phenix.real_space_refine
on Sun Aug 24 11:16:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nog_0468/08_2025/6nog_0468.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nog_0468/08_2025/6nog_0468.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nog_0468/08_2025/6nog_0468.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nog_0468/08_2025/6nog_0468.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nog_0468/08_2025/6nog_0468.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nog_0468/08_2025/6nog_0468.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     292      5.49       5
     S      27      5.16       5
     C    8489      2.51       5
     N    2751      2.21       5
     O    3370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14929
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 800
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "G"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 723
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "H"
      Number of atoms: 733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 733
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "L"
      Number of atoms: 593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 593
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "K"
      Number of atoms: 2431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2431
          Classifications: {'peptide': 302}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 288}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "I"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
  Time building chain proxies: 2.89, per 1000 atoms: 0.19
  Number of scatterers: 14929
  At special positions: 0
  Unit cell: (118.104, 138.32, 118.104, 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      27     16.00
     P     292     15.00
     O    3370      8.00
     N    2751      7.00
     C    8489      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 359.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2116

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 9 sheets defined
      63.2% alpha, 5.5% beta
      135 base pairs and 245 stacking pairs defined.
    Time for finding SS restraints: 1.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.843A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA A  75 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.700A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.913A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLY A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.925A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 113
      removed outlier: 3.604A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 4.103A  pdb=" N   ILE E 130 " --> pdb=" O   LEU E 126 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ARG E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY E 132 " --> pdb=" O   ARG E 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.768A  pdb=" N   GLY B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.417A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 4.095A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.586A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 50 through 75
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.820A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY F  94 " --> pdb=" O   LEU F  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.527A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 4.137A  pdb=" N   ASP C  72 " --> pdb=" O   ASN C  68 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.635A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 4.026A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.986A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU G  51 " --> pdb=" O   ALA G  47 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.747A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL G  87 " --> pdb=" O   LEU G  83 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG G  88 " --> pdb=" O   GLN G  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.524A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 46
      removed outlier: 3.783A  pdb=" N   VAL D  41 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   LYS D  46 " --> pdb=" O   TYR D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 83
      removed outlier: 3.653A  pdb=" N   SER D  60 " --> pdb=" O   SER D  56 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU D  80 " --> pdb=" O   GLU D  76 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA D  81 " --> pdb=" O   ALA D  77 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   HIS D  82 " --> pdb=" O   SER D  78 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   TYR D  83 " --> pdb=" O   ARG D  79 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.504A  pdb=" N   ARG D  99 " --> pdb=" O   GLN D  95 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU D 100 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU D 101 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU D 102 " --> pdb=" O   VAL D  98 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 122
      removed outlier: 4.504A  pdb=" N   THR D 119 " --> pdb=" O   THR D 115 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   CYS D 120 " --> pdb=" O   LYS D 116 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   TYR D 121 " --> pdb=" O   ALA D 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 46
      removed outlier: 3.769A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LYS H  46 " --> pdb=" O   TYR H  42 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 83
      removed outlier: 3.777A  pdb=" N   LEU H  80 " --> pdb=" O   GLU H  76 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA H  81 " --> pdb=" O   ALA H  77 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   HIS H  82 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 92 through 102
      removed outlier: 3.965A  pdb=" N   THR H  96 " --> pdb=" O   ARG H  92 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU H 100 " --> pdb=" O   THR H  96 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
      removed outlier: 3.848A  pdb=" N   CYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR H 122 " --> pdb=" O   VAL H 118 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 22 through 35
    Processing helix  chain 'L' and resid 37 through 39
      No H-bonds generated for 'chain 'L' and resid 37 through 39'
    Processing helix  chain 'L' and resid 55 through 60
      removed outlier: 3.577A  pdb=" N   TYR L  59 " --> pdb=" O   LEU L  56 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ASN L  60 " --> pdb=" O   SER L  57 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 33 through 48
    Processing helix  chain 'K' and resid 48 through 57
    Processing helix  chain 'K' and resid 67 through 91
    Processing helix  chain 'K' and resid 103 through 119
    Processing helix  chain 'K' and resid 140 through 151
      removed outlier: 3.518A  pdb=" N   VAL K 144 " --> pdb=" O   SER K 140 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 167 through 177
    Processing helix  chain 'K' and resid 188 through 210
    Processing helix  chain 'K' and resid 225 through 234
      removed outlier: 3.511A  pdb=" N   ARG K 229 " --> pdb=" O   SER K 225 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   GLU K 230 " --> pdb=" O   GLU K 226 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ARG K 231 " --> pdb=" O   GLU K 227 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 246 through 258
    Processing helix  chain 'K' and resid 286 through 289
    Processing helix  chain 'K' and resid 319 through 329
      removed outlier: 3.544A  pdb=" N   GLU K 323 " --> pdb=" O   ARG K 319 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97
      removed outlier: 7.099A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.709A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.510A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'L' and resid 12 through 16
      removed outlier: 3.512A  pdb=" N   LEU L  15 " --> pdb=" O   ILE L   3 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE L  45 " --> pdb=" O   LYS L  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 9
      removed outlier: 3.522A  pdb=" N   LEU K   7 " --> pdb=" O   TYR K  20 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AA9, first strand: chain 'K' and resid 216 through 220
      removed outlier: 6.225A  pdb=" N   HIS K 182 " --> pdb=" O   THR K 217 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   GLU K 219 " --> pdb=" O   HIS K 182 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   GLY K 184 " --> pdb=" O   GLU K 219 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   PHE K 159 " --> pdb=" O   TYR K 183 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   VAL K 185 " --> pdb=" O   PHE K 159 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ASP K 161 " --> pdb=" O   VAL K 185 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   VAL K 160 " --> pdb=" O   PHE K 239 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ILE K 238 " --> pdb=" O   VAL K 267 " (cutoff:3.500A)

    480 hydrogen bonds defined for protein.
    1407 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      350 hydrogen bonds
      700 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      245 stacking parallelities
  Total time for adding SS restraints: 2.20

  Time building geometry restraints manager: 1.22 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: 2744
        1.33 -     1.45: 5049
        1.45 -     1.57: 7375
        1.57 -     1.69: 583
        1.69 -     1.82: 47
  Bond restraints: 15798
  Sorted by residual:
  bond pdb=" N   PRO G  80 "
       pdb=" CD  PRO G  80 "
    ideal  model  delta    sigma   weight residual
    1.473  1.422  0.051 1.40e-02 5.10e+03 1.35e+01
  bond pdb=" C3'  DC J 126 "
       pdb=" O3'  DC J 126 "
    ideal  model  delta    sigma   weight residual
    1.422  1.495 -0.073 3.00e-02 1.11e+03 5.90e+00
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.494 -0.072 3.00e-02 1.11e+03 5.75e+00
  bond pdb=" C   HIS H  49 "
       pdb=" N   PRO H  50 "
    ideal  model  delta    sigma   weight residual
    1.336  1.308  0.028 1.20e-02 6.94e+03 5.60e+00
  bond pdb=" C   GLY G  46 "
       pdb=" N   ALA G  47 "
    ideal  model  delta    sigma   weight residual
    1.332  1.300  0.032 1.38e-02 5.25e+03 5.22e+00
  ... (remaining 15793 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 21640
        2.48 -     4.97: 856
        4.97 -     7.45: 80
        7.45 -     9.93: 21
        9.93 -    12.41: 4
  Bond angle restraints: 22601
  Sorted by residual:
  angle pdb=" C   ARG F  23 "
        pdb=" N   ASP F  24 "
        pdb=" CA  ASP F  24 "
      ideal   model   delta    sigma   weight residual
     122.46  129.87   -7.41 1.41e+00 5.03e-01 2.76e+01
  angle pdb=" N   GLY G 105 "
        pdb=" CA  GLY G 105 "
        pdb=" C   GLY G 105 "
      ideal   model   delta    sigma   weight residual
     113.18  124.85  -11.67 2.37e+00 1.78e-01 2.43e+01
  angle pdb=" C   ASP G  90 "
        pdb=" N   GLU G  91 "
        pdb=" CA  GLU G  91 "
      ideal   model   delta    sigma   weight residual
     120.54  127.15   -6.61 1.35e+00 5.49e-01 2.40e+01
  angle pdb=" N   GLY C  46 "
        pdb=" CA  GLY C  46 "
        pdb=" C   GLY C  46 "
      ideal   model   delta    sigma   weight residual
     114.66  120.63   -5.97 1.24e+00 6.50e-01 2.32e+01
  angle pdb=" N   ASP F  24 "
        pdb=" CA  ASP F  24 "
        pdb=" C   ASP F  24 "
      ideal   model   delta    sigma   weight residual
     111.30  117.58   -6.28 1.36e+00 5.41e-01 2.13e+01
  ... (remaining 22596 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.82: 7037
       31.82 -    63.65: 1668
       63.65 -    95.47: 50
       95.47 -   127.29: 0
      127.29 -   159.12: 3
  Dihedral angle restraints: 8758
    sinusoidal: 5489
      harmonic: 3269
  Sorted by residual:
  dihedral pdb=" CA  ARG A  63 "
           pdb=" C   ARG A  63 "
           pdb=" N   LYS A  64 "
           pdb=" CA  LYS A  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.77  -28.23     0      5.00e+00 4.00e-02 3.19e+01
  dihedral pdb=" CA  ARG E  63 "
           pdb=" C   ARG E  63 "
           pdb=" N   LYS E  64 "
           pdb=" CA  LYS E  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.74  -24.26     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.19  -22.81     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 8755 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 2041
       0.071 -    0.142: 445
       0.142 -    0.213: 63
       0.213 -    0.284: 12
       0.284 -    0.355: 8
  Chirality restraints: 2569
  Sorted by residual:
  chirality pdb=" CG  LEU K 107 "
            pdb=" CB  LEU K 107 "
            pdb=" CD1 LEU K 107 "
            pdb=" CD2 LEU K 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.94    0.36 2.00e-01 2.50e+01 3.15e+00
  chirality pdb=" CB  ILE K 151 "
            pdb=" CA  ILE K 151 "
            pdb=" CG1 ILE K 151 "
            pdb=" CG2 ILE K 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CA  LEU K 299 "
            pdb=" N   LEU K 299 "
            pdb=" C   LEU K 299 "
            pdb=" CB  LEU K 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.68e+00
  ... (remaining 2566 not shown)

  Planarity restraints: 1855
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "   -0.048 5.00e-02 4.00e+02   7.15e-02 8.19e+00
        pdb=" N   PRO H 103 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K 266 "    0.013 2.00e-02 2.50e+03   2.70e-02 7.31e+00
        pdb=" C   ILE K 266 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ILE K 266 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL K 267 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  91 "   -0.036 2.00e-02 2.50e+03   1.59e-02 6.96e+00
        pdb=" N9   DA I  91 "    0.030 2.00e-02 2.50e+03
        pdb=" C8   DA I  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N7   DA I  91 "    0.011 2.00e-02 2.50e+03
        pdb=" C5   DA I  91 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6   DA I  91 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6   DA I  91 "   -0.012 2.00e-02 2.50e+03
        pdb=" N1   DA I  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  91 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  91 "    0.009 2.00e-02 2.50e+03
        pdb=" C4   DA I  91 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1852 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2724
        2.77 -     3.30: 12860
        3.30 -     3.84: 28212
        3.84 -     4.37: 30410
        4.37 -     4.90: 43971
  Nonbonded interactions: 118177
  Sorted by model distance:
  nonbonded pdb=" OG1 THR K 154 "
            pdb=" OD1 ASP K 155 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   ASP K 161 "
            pdb=" OG  SER K 164 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OD1 ASN K 242 "
            pdb=" OG  SER K 268 "
     model   vdw
     2.327 3.040
  ... (remaining 118172 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 25 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 14 through 117)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 32 through 124)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.670
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
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      :  0.009   0.073  15798  Z= 0.432
  Angle     :  1.118  12.415  22601  Z= 0.660
  Chirality :  0.062   0.355   2569
  Planarity :  0.008   0.072   1855
  Dihedral  : 26.638 159.118   6642
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.67 %
    Favored  : 91.49 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.83 (0.22), residues: 1098
  helix: -1.16 (0.17), residues: 634
  sheet:  0.01 (0.56), residues: 79
  loop : -1.28 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG K 203 
 TYR   0.030   0.004   TYR K  27 
 PHE   0.032   0.004   PHE K 159 
 TRP   0.030   0.004   TRP K 208 
 HIS   0.008   0.003   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00946 (15798)
  covalent geometry    : angle       1.11808 (22601)
  hydrogen bonds       : bond        0.15789 (  830)
  hydrogen bonds       : angle       5.31407 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  394 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 386
  time to evaluate  : 0.318 
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   60 LEU cc_start: 0.8253 (mt) cc_final: 0.7951 (mt)
REVERT: A   80 THR cc_start: 0.8160 (t) cc_final: 0.7703 (t)
REVERT: A   86 SER cc_start: 0.8987 (m) cc_final: 0.8662 (t)
REVERT: A  108 ASN cc_start: 0.8699 (t0) cc_final: 0.8482 (t0)
REVERT: E   41 TYR cc_start: 0.8336 (m-80) cc_final: 0.8041 (m-80)
REVERT: F   25 ASN cc_start: 0.8048 (m110) cc_final: 0.7809 (m-40)
REVERT: F   63 GLU cc_start: 0.8364 (tt0) cc_final: 0.8164 (tt0)
REVERT: F   88 TYR cc_start: 0.8458 (m-10) cc_final: 0.8190 (m-10)
REVERT: C   68 ASN cc_start: 0.8668 (t0) cc_final: 0.8417 (t0)
REVERT: G   68 ASN cc_start: 0.8479 (m-40) cc_final: 0.7210 (m-40)
REVERT: G   74 LYS cc_start: 0.8702 (mttm) cc_final: 0.8368 (mtmm)
REVERT: D   79 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8153 (mtm-85)
REVERT: D  105 GLU cc_start: 0.7944 (tp30) cc_final: 0.7667 (tm-30)
REVERT: D  109 HIS cc_start: 0.8099 (m90) cc_final: 0.7611 (m-70)
REVERT: D  121 TYR cc_start: 0.8029 (t80) cc_final: 0.7672 (t80)
REVERT: H   59 MET cc_start: 0.9006 (tpp) cc_final: 0.8615 (tpp)
REVERT: H   85 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8415 (mmtt)
REVERT: L    6 LYS cc_start: 0.8458 (tttt) cc_final: 0.7744 (mmtt)
REVERT: L    8 LEU cc_start: 0.4657 (mm) cc_final: 0.4074 (tt)
REVERT: L   29 LYS cc_start: 0.8544 (mttt) cc_final: 0.8217 (tptp)
REVERT: L   39 ASP cc_start: 0.7768 (p0) cc_final: 0.7447 (m-30)
REVERT: L   71 LEU cc_start: 0.6967 (mt) cc_final: 0.6582 (mt)
REVERT: K   27 TYR cc_start: 0.4974 (m-80) cc_final: 0.3654 (t80)
REVERT: K   49 PRO cc_start: 0.6899 (Cg_exo) cc_final: 0.6654 (Cg_endo)
  outliers start: 8
  outliers final: 1
  residues processed: 389
  average time/residue: 0.1561
  time to fit residues: 79.6179
Evaluate side-chains
  185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   46 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
F  25 ASN
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  89 ASN
D  49 HIS
D  84 ASN
D  95 GLN
** L  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 113 GLN
** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 251 HIS
K 252 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.103735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.072036 restraints weight = 44329.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.072888 restraints weight = 31104.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.073138 restraints weight = 21737.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.073152 restraints weight = 20633.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.073159 restraints weight = 19157.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  15798  Z= 0.173
  Angle     :  0.637   7.192  22601  Z= 0.373
  Chirality :  0.037   0.174   2569
  Planarity :  0.005   0.056   1855
  Dihedral  : 29.264 159.581   4429
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 14.92 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1098
  helix:  0.90 (0.20), residues: 655
  sheet:  0.61 (0.60), residues: 79
  loop : -0.71 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  78 
 TYR   0.015   0.002   TYR H  83 
 PHE   0.030   0.002   PHE L   4 
 TRP   0.026   0.003   TRP K 228 
 HIS   0.008   0.001   HIS K 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (15798)
  covalent geometry    : angle       0.63650 (22601)
  hydrogen bonds       : bond        0.05253 (  830)
  hydrogen bonds       : angle       3.48043 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 214
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   41 TYR cc_start: 0.8559 (m-80) cc_final: 0.8304 (m-80)
REVERT: E  105 GLU cc_start: 0.7776 (tp30) cc_final: 0.7575 (tp30)
REVERT: B   74 GLU cc_start: 0.7598 (tp30) cc_final: 0.7315 (tp30)
REVERT: F   25 ASN cc_start: 0.8133 (m-40) cc_final: 0.7825 (m110)
REVERT: F   63 GLU cc_start: 0.7920 (tt0) cc_final: 0.7694 (tt0)
REVERT: F   82 THR cc_start: 0.9041 (p) cc_final: 0.8598 (m)
REVERT: F   84 MET cc_start: 0.7620 (tpp) cc_final: 0.7416 (tpp)
REVERT: C   61 GLU cc_start: 0.8073 (tt0) cc_final: 0.7831 (tt0)
REVERT: G   16 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.8890 (p)
REVERT: G   64 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7268 (tm-30)
REVERT: D  121 TYR cc_start: 0.8052 (t80) cc_final: 0.7817 (t80)
REVERT: H   34 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8539 (mmtm)
REVERT: H   59 MET cc_start: 0.8734 (tpp) cc_final: 0.8530 (tpp)
REVERT: H   91 SER cc_start: 0.8558 (t) cc_final: 0.8277 (p)
REVERT: L    6 LYS cc_start: 0.8327 (tttt) cc_final: 0.7739 (mmtt)
REVERT: L    8 LEU cc_start: 0.4655 (mm) cc_final: 0.4257 (tt)
REVERT: L   39 ASP cc_start: 0.7391 (p0) cc_final: 0.7141 (t0)
REVERT: K   31 HIS cc_start: 0.4847 (OUTLIER) cc_final: 0.4262 (m90)
REVERT: K   49 PRO cc_start: 0.6758 (Cg_exo) cc_final: 0.6491 (Cg_endo)
  outliers start: 38
  outliers final: 18
  residues processed: 240
  average time/residue: 0.1132
  time to fit residues: 39.4982
Evaluate side-chains
  179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain H residue   44 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  116 LYS
Chi-restraints excluded: chain L residue   12 THR
Chi-restraints excluded: chain L residue   36 ILE
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   69 LEU
Chi-restraints excluded: chain K residue   31 HIS
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 111 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 89 optimal weight:    0.0000
   chunk 23 optimal weight:    2.9990
   chunk 135 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 108 optimal weight:   10.0000
   chunk 116 optimal weight:    7.9990
   overall best weight:    3.1992

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
F  25 ASN
C  38 ASN
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 ASN
D  47 GLN
K  31 HIS
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 251 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.097919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.064787 restraints weight = 44084.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.065011 restraints weight = 34929.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.065042 restraints weight = 27116.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.065350 restraints weight = 24227.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.065388 restraints weight = 22396.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.4340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  15798  Z= 0.280
  Angle     :  0.696   7.701  22601  Z= 0.399
  Chirality :  0.041   0.167   2569
  Planarity :  0.005   0.049   1855
  Dihedral  : 29.214 154.259   4428
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 18.28 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.25), residues: 1098
  helix:  1.17 (0.20), residues: 660
  sheet:  0.59 (0.57), residues: 79
  loop : -0.47 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  42 
 TYR   0.029   0.003   TYR D  83 
 PHE   0.015   0.002   PHE C  25 
 TRP   0.032   0.003   TRP K 228 
 HIS   0.010   0.002   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 (15798)
  covalent geometry    : angle       0.69583 (22601)
  hydrogen bonds       : bond        0.05682 (  830)
  hydrogen bonds       : angle       3.65451 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 157
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9261 (m) cc_final: 0.8987 (t)
REVERT: E  105 GLU cc_start: 0.7846 (tp30) cc_final: 0.7505 (tp30)
REVERT: F   63 GLU cc_start: 0.8016 (tt0) cc_final: 0.7796 (tt0)
REVERT: C   61 GLU cc_start: 0.8257 (tt0) cc_final: 0.7954 (tt0)
REVERT: C   84 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8259 (tt0)
REVERT: G   56 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7906 (tm-30)
REVERT: G   64 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: G  110 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7866 (m110)
REVERT: H   42 TYR cc_start: 0.7958 (t80) cc_final: 0.7732 (t80)
REVERT: H   59 MET cc_start: 0.8784 (tpp) cc_final: 0.8393 (tpp)
REVERT: L    6 LYS cc_start: 0.8353 (tttt) cc_final: 0.7693 (mmtp)
REVERT: L    8 LEU cc_start: 0.4623 (mm) cc_final: 0.4060 (tt)
REVERT: L   33 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5667 (ptmt)
REVERT: L   39 ASP cc_start: 0.7459 (p0) cc_final: 0.7013 (t0)
REVERT: K   31 HIS cc_start: 0.4380 (OUTLIER) cc_final: 0.4027 (m90)
REVERT: K  317 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8219 (mm)
  outliers start: 45
  outliers final: 23
  residues processed: 186
  average time/residue: 0.1036
  time to fit residues: 29.0240
Evaluate side-chains
  164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain E residue   85 GLN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  113 SER
Chi-restraints excluded: chain D residue   51 ASP
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue   82 HIS
Chi-restraints excluded: chain H residue  116 LYS
Chi-restraints excluded: chain L residue   13 ILE
Chi-restraints excluded: chain L residue   33 LYS
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   69 LEU
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue   31 HIS
Chi-restraints excluded: chain K residue  238 ILE
Chi-restraints excluded: chain K residue  317 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   chunk 123 optimal weight:   10.0000
   chunk 120 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 80 optimal weight:    4.9990
   chunk 133 optimal weight:    6.9990
   chunk 112 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 109 HIS
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 251 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.098417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.065262 restraints weight = 43562.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.065383 restraints weight = 32278.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.065518 restraints weight = 24243.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.065814 restraints weight = 22808.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.065866 restraints weight = 20678.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15798  Z= 0.194
  Angle     :  0.609   6.949  22601  Z= 0.356
  Chirality :  0.037   0.155   2569
  Planarity :  0.004   0.039   1855
  Dihedral  : 29.042 154.848   4428
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 19.33 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1098
  helix:  1.54 (0.20), residues: 659
  sheet:  0.62 (0.57), residues: 79
  loop : -0.34 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  29 
 TYR   0.029   0.002   TYR D  83 
 PHE   0.011   0.001   PHE K 326 
 TRP   0.028   0.002   TRP K 228 
 HIS   0.011   0.001   HIS K  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (15798)
  covalent geometry    : angle       0.60945 (22601)
  hydrogen bonds       : bond        0.04757 (  830)
  hydrogen bonds       : angle       3.42449 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9184 (m) cc_final: 0.8869 (t)
REVERT: E  105 GLU cc_start: 0.7823 (tp30) cc_final: 0.7485 (tp30)
REVERT: E  133 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7952 (mt-10)
REVERT: F   63 GLU cc_start: 0.7890 (tt0) cc_final: 0.7677 (tt0)
REVERT: F   84 MET cc_start: 0.7854 (tpp) cc_final: 0.7592 (tpp)
REVERT: C   61 GLU cc_start: 0.8164 (tt0) cc_final: 0.7911 (tt0)
REVERT: G   56 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7745 (tm-30)
REVERT: G   64 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: G   68 ASN cc_start: 0.8326 (m-40) cc_final: 0.7713 (t0)
REVERT: H   42 TYR cc_start: 0.7913 (t80) cc_final: 0.7653 (t80)
REVERT: H  116 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8397 (ttmm)
REVERT: L    6 LYS cc_start: 0.8339 (tttt) cc_final: 0.7606 (mptt)
REVERT: L    8 LEU cc_start: 0.4685 (mm) cc_final: 0.4083 (tt)
REVERT: L   15 LEU cc_start: 0.6126 (mp) cc_final: 0.5274 (tt)
REVERT: L   39 ASP cc_start: 0.7253 (p0) cc_final: 0.6920 (t0)
REVERT: L   69 LEU cc_start: 0.5873 (tp) cc_final: 0.5490 (tp)
REVERT: K   31 HIS cc_start: 0.4215 (OUTLIER) cc_final: 0.3967 (m90)
REVERT: K  149 ASP cc_start: 0.7671 (m-30) cc_final: 0.7412 (p0)
REVERT: K  238 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8742 (mp)
  outliers start: 36
  outliers final: 23
  residues processed: 175
  average time/residue: 0.0937
  time to fit residues: 25.6415
Evaluate side-chains
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain H residue  116 LYS
Chi-restraints excluded: chain L residue   13 ILE
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue   31 HIS
Chi-restraints excluded: chain K residue  151 ILE
Chi-restraints excluded: chain K residue  217 THR
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 39 optimal weight:    0.0980
   chunk 89 optimal weight:    0.0040
   chunk 9 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 117 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.101318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.068536 restraints weight = 43814.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.068538 restraints weight = 29365.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.069021 restraints weight = 21773.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.069066 restraints weight = 20372.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.069105 restraints weight = 18683.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.4967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15798  Z= 0.141
  Angle     :  0.563   8.521  22601  Z= 0.330
  Chirality :  0.034   0.143   2569
  Planarity :  0.004   0.042   1855
  Dihedral  : 28.809 154.093   4428
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.27 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.26), residues: 1098
  helix:  1.84 (0.20), residues: 654
  sheet:  0.50 (0.57), residues: 81
  loop : -0.06 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  54 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.009   0.001   PHE K 326 
 TRP   0.017   0.001   TRP K 228 
 HIS   0.006   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (15798)
  covalent geometry    : angle       0.56288 (22601)
  hydrogen bonds       : bond        0.03915 (  830)
  hydrogen bonds       : angle       3.15252 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9421 (t0) cc_final: 0.9148 (t0)
REVERT: E   94 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7525 (mm-30)
REVERT: E  105 GLU cc_start: 0.7947 (tp30) cc_final: 0.7601 (tp30)
REVERT: F   25 ASN cc_start: 0.8610 (m110) cc_final: 0.8116 (m110)
REVERT: C   61 GLU cc_start: 0.8216 (tt0) cc_final: 0.7930 (tt0)
REVERT: C   84 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8132 (tt0)
REVERT: G   56 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7717 (tm-30)
REVERT: G   68 ASN cc_start: 0.8168 (m-40) cc_final: 0.7872 (t0)
REVERT: G  110 ASN cc_start: 0.8196 (m-40) cc_final: 0.7910 (m-40)
REVERT: D   76 GLU cc_start: 0.8999 (tp30) cc_final: 0.8775 (tp30)
REVERT: H   59 MET cc_start: 0.9043 (tpp) cc_final: 0.8792 (tpp)
REVERT: H  108 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8425 (mttp)
REVERT: L    6 LYS cc_start: 0.8440 (tttt) cc_final: 0.7662 (mmtp)
REVERT: L   15 LEU cc_start: 0.6349 (mp) cc_final: 0.5216 (tt)
REVERT: L   30 ILE cc_start: 0.8403 (mm) cc_final: 0.8048 (mm)
REVERT: L   33 LYS cc_start: 0.6537 (pptt) cc_final: 0.5187 (ptmm)
REVERT: L   39 ASP cc_start: 0.7346 (p0) cc_final: 0.7086 (t0)
REVERT: K   31 HIS cc_start: 0.4777 (m-70) cc_final: 0.4120 (m90)
REVERT: K  238 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8787 (mp)
  outliers start: 29
  outliers final: 14
  residues processed: 179
  average time/residue: 0.0950
  time to fit residues: 26.2254
Evaluate side-chains
  162 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain E residue   85 GLN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue   55 MET
Chi-restraints excluded: chain K residue  151 ILE
Chi-restraints excluded: chain K residue  217 THR
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 86 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 71 optimal weight:   40.0000
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 40 optimal weight:    0.8980
   chunk 55 optimal weight:    5.9990
   chunk 115 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    0.1980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
E 108 ASN
F  75 HIS
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.099502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.066888 restraints weight = 43375.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.068504 restraints weight = 33219.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.068310 restraints weight = 23365.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.068471 restraints weight = 21091.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.068427 restraints weight = 20092.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.5152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15798  Z= 0.174
  Angle     :  0.580   7.162  22601  Z= 0.339
  Chirality :  0.035   0.153   2569
  Planarity :  0.004   0.039   1855
  Dihedral  : 28.905 153.337   4428
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.22 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.26), residues: 1098
  helix:  1.84 (0.20), residues: 657
  sheet:  0.71 (0.57), residues: 79
  loop : -0.06 (0.36), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  54 
 TYR   0.027   0.002   TYR D  83 
 PHE   0.016   0.001   PHE E  84 
 TRP   0.017   0.001   TRP K 228 
 HIS   0.005   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (15798)
  covalent geometry    : angle       0.58041 (22601)
  hydrogen bonds       : bond        0.04345 (  830)
  hydrogen bonds       : angle       3.26301 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 144
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9442 (t0) cc_final: 0.9123 (t0)
REVERT: E  105 GLU cc_start: 0.7927 (tp30) cc_final: 0.7585 (tp30)
REVERT: E  133 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7932 (mt-10)
REVERT: F   25 ASN cc_start: 0.8628 (m110) cc_final: 0.8103 (m110)
REVERT: C   61 GLU cc_start: 0.8224 (tt0) cc_final: 0.7958 (tt0)
REVERT: C   84 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8273 (tt0)
REVERT: G   68 ASN cc_start: 0.8285 (m-40) cc_final: 0.7882 (t0)
REVERT: D  121 TYR cc_start: 0.8572 (t80) cc_final: 0.8365 (t80)
REVERT: H   59 MET cc_start: 0.8992 (tpp) cc_final: 0.8788 (tpp)
REVERT: H  108 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8246 (mtmm)
REVERT: L    6 LYS cc_start: 0.8352 (tttt) cc_final: 0.7775 (mmtp)
REVERT: L    8 LEU cc_start: 0.4716 (mm) cc_final: 0.4101 (tt)
REVERT: L   39 ASP cc_start: 0.7316 (p0) cc_final: 0.7039 (t0)
REVERT: K   31 HIS cc_start: 0.4434 (m-70) cc_final: 0.3880 (m90)
REVERT: K  238 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8764 (mp)
  outliers start: 29
  outliers final: 19
  residues processed: 163
  average time/residue: 0.0970
  time to fit residues: 24.1366
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain E residue   85 GLN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue  151 ILE
Chi-restraints excluded: chain K residue  217 THR
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 13 optimal weight:    0.3980
   chunk 121 optimal weight:   10.0000
   chunk 125 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 126 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 122 optimal weight:   10.0000
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  31 HIS
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.099442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.066980 restraints weight = 43182.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.066879 restraints weight = 27642.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.067169 restraints weight = 23493.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.067387 restraints weight = 21975.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.067369 restraints weight = 19719.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.5389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15798  Z= 0.171
  Angle     :  0.581   8.810  22601  Z= 0.337
  Chirality :  0.035   0.160   2569
  Planarity :  0.004   0.040   1855
  Dihedral  : 28.895 152.709   4428
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.53 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.26), residues: 1098
  helix:  1.77 (0.20), residues: 667
  sheet:  0.82 (0.59), residues: 79
  loop :  0.03 (0.36), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 116 
 TYR   0.017   0.001   TYR B  88 
 PHE   0.007   0.001   PHE K 326 
 TRP   0.011   0.001   TRP K 228 
 HIS   0.005   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (15798)
  covalent geometry    : angle       0.58116 (22601)
  hydrogen bonds       : bond        0.04338 (  830)
  hydrogen bonds       : angle       3.28500 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9433 (t0) cc_final: 0.9124 (t0)
REVERT: E  105 GLU cc_start: 0.8020 (tp30) cc_final: 0.7658 (tp30)
REVERT: E  133 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8103 (mt-10)
REVERT: C   61 GLU cc_start: 0.8238 (tt0) cc_final: 0.7979 (tt0)
REVERT: C   84 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8305 (tt0)
REVERT: G   68 ASN cc_start: 0.8325 (m-40) cc_final: 0.7888 (t0)
REVERT: H   40 TYR cc_start: 0.9143 (m-80) cc_final: 0.8920 (m-80)
REVERT: H  108 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8268 (mtmm)
REVERT: L    6 LYS cc_start: 0.8447 (tttt) cc_final: 0.7684 (mmtp)
REVERT: L    8 LEU cc_start: 0.4738 (mm) cc_final: 0.4108 (tt)
REVERT: L   33 LYS cc_start: 0.6574 (pptt) cc_final: 0.4966 (ptmm)
REVERT: L   39 ASP cc_start: 0.7406 (p0) cc_final: 0.7158 (t0)
REVERT: K   31 HIS cc_start: 0.4289 (OUTLIER) cc_final: 0.4003 (m90)
REVERT: K  238 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8801 (mp)
  outliers start: 29
  outliers final: 18
  residues processed: 154
  average time/residue: 0.0982
  time to fit residues: 23.1100
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain E residue   85 GLN
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain E residue  133 GLU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain D residue   91 SER
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue   31 HIS
Chi-restraints excluded: chain K residue  151 ILE
Chi-restraints excluded: chain K residue  217 THR
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 71 optimal weight:   30.0000
   chunk 15 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 133 optimal weight:    6.9990
   chunk 100 optimal weight:    0.8980
   chunk 9 optimal weight:   10.0000
   chunk 130 optimal weight:    5.9990
   chunk 56 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K  31 HIS
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.100736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.068318 restraints weight = 43953.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.069657 restraints weight = 32698.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.069481 restraints weight = 24107.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.069589 restraints weight = 22608.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.069587 restraints weight = 20660.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.5499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15798  Z= 0.144
  Angle     :  0.564   8.434  22601  Z= 0.327
  Chirality :  0.034   0.173   2569
  Planarity :  0.004   0.039   1855
  Dihedral  : 28.816 152.157   4428
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 22.69 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.26), residues: 1098
  helix:  1.90 (0.20), residues: 660
  sheet:  0.79 (0.56), residues: 79
  loop :  0.01 (0.36), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 116 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.012   0.001   PHE K 243 
 TRP   0.009   0.001   TRP K 228 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (15798)
  covalent geometry    : angle       0.56383 (22601)
  hydrogen bonds       : bond        0.04028 (  830)
  hydrogen bonds       : angle       3.18467 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 145
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9391 (t0) cc_final: 0.9119 (t0)
REVERT: E  105 GLU cc_start: 0.8011 (tp30) cc_final: 0.7649 (tp30)
REVERT: F   25 ASN cc_start: 0.8708 (m110) cc_final: 0.8178 (m110)
REVERT: C   61 GLU cc_start: 0.8223 (tt0) cc_final: 0.7983 (tt0)
REVERT: C   84 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8263 (tt0)
REVERT: G   24 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7845 (mm110)
REVERT: G   68 ASN cc_start: 0.8283 (m-40) cc_final: 0.8020 (t0)
REVERT: D   36 SER cc_start: 0.9086 (t) cc_final: 0.8631 (p)
REVERT: H   59 MET cc_start: 0.8924 (tpp) cc_final: 0.8566 (tpp)
REVERT: L    6 LYS cc_start: 0.8384 (tttt) cc_final: 0.7720 (mmtp)
REVERT: L    8 LEU cc_start: 0.4790 (mm) cc_final: 0.4161 (tt)
REVERT: L   33 LYS cc_start: 0.6387 (pptt) cc_final: 0.4852 (ptmm)
REVERT: L   39 ASP cc_start: 0.7104 (p0) cc_final: 0.6896 (t0)
REVERT: K  238 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8769 (mp)
  outliers start: 23
  outliers final: 15
  residues processed: 159
  average time/residue: 0.0925
  time to fit residues: 22.9024
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue  217 THR
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:   10.0000
   chunk 114 optimal weight:    7.9990
   chunk 108 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 133 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.100467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.068015 restraints weight = 44056.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.069025 restraints weight = 33966.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.068942 restraints weight = 25133.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.069099 restraints weight = 22761.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.069110 restraints weight = 20888.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.5604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15798  Z= 0.153
  Angle     :  0.567   8.718  22601  Z= 0.329
  Chirality :  0.035   0.199   2569
  Planarity :  0.004   0.039   1855
  Dihedral  : 28.810 151.841   4428
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 22.90 %
    Favored  : 74.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.26), residues: 1098
  helix:  1.86 (0.20), residues: 664
  sheet:  0.81 (0.55), residues: 79
  loop : -0.06 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 116 
 TYR   0.019   0.001   TYR D  40 
 PHE   0.010   0.001   PHE K 243 
 TRP   0.008   0.001   TRP K 228 
 HIS   0.008   0.001   HIS K 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (15798)
  covalent geometry    : angle       0.56689 (22601)
  hydrogen bonds       : bond        0.04121 (  830)
  hydrogen bonds       : angle       3.21048 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9441 (t0) cc_final: 0.9151 (t0)
REVERT: E  105 GLU cc_start: 0.8043 (tp30) cc_final: 0.7697 (tp30)
REVERT: C   61 GLU cc_start: 0.8216 (tt0) cc_final: 0.7958 (tt0)
REVERT: C   84 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8298 (tt0)
REVERT: G   68 ASN cc_start: 0.8290 (m-40) cc_final: 0.8016 (t0)
REVERT: D   36 SER cc_start: 0.9071 (t) cc_final: 0.8620 (p)
REVERT: H   59 MET cc_start: 0.8921 (tpp) cc_final: 0.8566 (tpp)
REVERT: H  108 LYS cc_start: 0.8637 (mttp) cc_final: 0.8287 (mtmt)
REVERT: L    6 LYS cc_start: 0.8366 (tttt) cc_final: 0.7695 (mmtp)
REVERT: L    8 LEU cc_start: 0.4800 (mm) cc_final: 0.4197 (tt)
REVERT: L   33 LYS cc_start: 0.6617 (pptt) cc_final: 0.5027 (ptmm)
REVERT: K  238 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8768 (mp)
  outliers start: 22
  outliers final: 16
  residues processed: 157
  average time/residue: 0.0966
  time to fit residues: 23.2675
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain E residue   85 GLN
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue  217 THR
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 112 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 92 optimal weight:    0.3980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.101195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068419 restraints weight = 43818.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.068718 restraints weight = 30560.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.069307 restraints weight = 21610.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.069269 restraints weight = 19646.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.069316 restraints weight = 18293.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.5736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15798  Z= 0.142
  Angle     :  0.567   8.490  22601  Z= 0.328
  Chirality :  0.034   0.196   2569
  Planarity :  0.004   0.041   1855
  Dihedral  : 28.735 151.355   4428
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.05 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.26), residues: 1098
  helix:  1.94 (0.20), residues: 664
  sheet:  0.92 (0.56), residues: 79
  loop : -0.00 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 116 
 TYR   0.017   0.001   TYR B  88 
 PHE   0.008   0.001   PHE K 243 
 TRP   0.021   0.001   TRP K  43 
 HIS   0.007   0.001   HIS K 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (15798)
  covalent geometry    : angle       0.56671 (22601)
  hydrogen bonds       : bond        0.03944 (  830)
  hydrogen bonds       : angle       3.17083 ( 2107)

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASN cc_start: 0.9403 (t0) cc_final: 0.9102 (t0)
REVERT: E  105 GLU cc_start: 0.8052 (tp30) cc_final: 0.7716 (tp30)
REVERT: F   25 ASN cc_start: 0.8709 (m110) cc_final: 0.8248 (m110)
REVERT: F   84 MET cc_start: 0.7961 (tpp) cc_final: 0.7494 (tpp)
REVERT: C   56 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7111 (tm-30)
REVERT: C   84 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8297 (tt0)
REVERT: G   24 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7651 (mm110)
REVERT: G   68 ASN cc_start: 0.8259 (m-40) cc_final: 0.8019 (t0)
REVERT: D   36 SER cc_start: 0.9056 (t) cc_final: 0.8655 (p)
REVERT: H   59 MET cc_start: 0.8918 (tpp) cc_final: 0.8580 (tpp)
REVERT: H  108 LYS cc_start: 0.8583 (mttp) cc_final: 0.8255 (mtmt)
REVERT: L    6 LYS cc_start: 0.8423 (tttt) cc_final: 0.7709 (mmtp)
REVERT: L    8 LEU cc_start: 0.4797 (mm) cc_final: 0.4202 (tt)
REVERT: L   33 LYS cc_start: 0.6700 (pptt) cc_final: 0.5194 (ptmm)
REVERT: K  238 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8764 (mp)
  outliers start: 19
  outliers final: 15
  residues processed: 159
  average time/residue: 0.0981
  time to fit residues: 23.5411
Evaluate side-chains
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain E residue  112 ILE
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain G residue   24 GLN
Chi-restraints excluded: chain H residue   51 ASP
Chi-restraints excluded: chain L residue    5 VAL
Chi-restraints excluded: chain L residue   44 ILE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain K residue  217 THR
Chi-restraints excluded: chain K residue  238 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 130 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   chunk 114 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 134 optimal weight:    7.9990
   chunk 133 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN
** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.101243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.068953 restraints weight = 43767.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.069796 restraints weight = 33838.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.069731 restraints weight = 25102.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.069994 restraints weight = 22404.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.069973 restraints weight = 21082.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.5732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  15798  Z= 0.168
  Angle     :  0.766  59.199  22601  Z= 0.455
  Chirality :  0.035   0.183   2569
  Planarity :  0.004   0.041   1855
  Dihedral  : 28.734 151.355   4428
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 24.26 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.26), residues: 1098
  helix:  1.94 (0.20), residues: 664
  sheet:  0.91 (0.55), residues: 79
  loop : -0.01 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 116 
 TYR   0.016   0.001   TYR B  88 
 PHE   0.006   0.001   PHE E  78 
 TRP   0.017   0.001   TRP K  43 
 HIS   0.006   0.001   HIS K 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (15798)
  covalent geometry    : angle       0.76583 (22601)
  hydrogen bonds       : bond        0.03952 (  830)
  hydrogen bonds       : angle       3.16851 ( 2107)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1829.05 seconds
wall clock time: 32 minutes 19.99 seconds (1939.99 seconds total)