Starting phenix.real_space_refine
on Wed Mar 12 23:21:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjl_33231/03_2025/7xjl_33231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjl_33231/03_2025/7xjl_33231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2025/7xjl_33231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2025/7xjl_33231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2025/7xjl_33231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjl_33231/03_2025/7xjl_33231.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.090
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5453      2.51       5
     N    1456      2.21       5
     O    1564      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8527
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 109
          Classifications: {'peptide': 14}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1750
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 81
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 55
    Chain: "C"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2471
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 160
          Unresolved non-hydrogen dihedrals: 104
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 98
    Chain: "D"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1712
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "F"
      Number of atoms: 2132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2132
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 55
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 44
  Time building chain proxies: 5.27, per 1000 atoms: 0.62
  Number of scatterers: 8527
  At special positions: 0
  Unit cell: (92.395, 119.57, 118.483, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1564      8.00
     N    1456      7.00
     C    5453      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  98 " - pdb=" SG  CYS F 175 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.26
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.5% alpha, 23.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
    Processing helix  chain 'B' and resid 6 through 32
      removed outlier: 3.757A  pdb=" N   ARG B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.557A  pdb=" N   MET B  53 " --> pdb=" O   ILE B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 99
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 3.512A  pdb=" N   LEU B 134 " --> pdb=" O   ASN B 131 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ARG B 135 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 131 through 135'
    Processing helix  chain 'B' and resid 145 through 156
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.895A  pdb=" N   TYR B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 183 through 203
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 4.139A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 26
      removed outlier: 3.654A  pdb=" N   ALA C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 12 through 24
      removed outlier: 3.731A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.534A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
      removed outlier: 3.767A  pdb=" N   ASP D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 48'
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.563A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.508A  pdb=" N   ASP E  90 " --> pdb=" O   ARG E  87 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 87 through 91'
    Processing helix  chain 'F' and resid 24 through 53
      Proline residue:  F  29  - end of helix
    Processing helix  chain 'F' and resid 58 through 88
      Proline residue:  F  80  - end of helix
      removed outlier: 4.786A  pdb=" N   ILE F  85 " --> pdb=" O   PHE F  81 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   TYR F  86 " --> pdb=" O   GLN F  82 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 129
      removed outlier: 4.163A  pdb=" N   LEU F  97 " --> pdb=" O   PHE F  93 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   CYS F  98 " --> pdb=" O   GLY F  94 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS F  99 " --> pdb=" O   SER F  95 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   HIS F 102 " --> pdb=" O   CYS F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 131 through 136
      removed outlier: 3.807A  pdb=" N   GLU F 135 " --> pdb=" O   HIS F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 138 through 158
    Processing helix  chain 'F' and resid 159 through 163
    Processing helix  chain 'F' and resid 180 through 196
      removed outlier: 3.793A  pdb=" N   ALA F 186 " --> pdb=" O   PRO F 182 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 215
    Processing helix  chain 'F' and resid 225 through 261
      removed outlier: 3.811A  pdb=" N   TRP F 249 " --> pdb=" O   PHE F 245 " (cutoff:3.500A)
      Proline residue:  F 251  - end of helix
    Processing helix  chain 'F' and resid 267 through 293
      removed outlier: 3.863A  pdb=" N   SER F 285 " --> pdb=" O   SER F 281 " (cutoff:3.500A)
      Proline residue:  F 289  - end of helix
    Processing helix  chain 'F' and resid 296 through 307
      removed outlier: 4.032A  pdb=" N   THR F 305 " --> pdb=" O   LYS F 301 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE F 306 " --> pdb=" O   GLY F 302 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS F 307 " --> pdb=" O   PHE F 303 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76
      removed outlier: 4.848A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ARG B  35 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 8.490A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 4.112A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LEU C 336 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.665A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105
      removed outlier: 3.740A  pdb=" N   GLY C 115 " --> pdb=" O   THR C 102 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ALA C 113 " --> pdb=" O   ALA C 104 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 148 through 151
      removed outlier: 5.947A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191
      removed outlier: 3.660A  pdb=" N   GLY C 202 " --> pdb=" O   SER C 189 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.703A  pdb=" N   SER C 245 " --> pdb=" O   THR C 249 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   THR C 249 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LEU C 252 " --> pdb=" O   MET C 262 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 4.016A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.849A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 4.279A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.613A  pdb=" N   ILE E 177 " --> pdb=" O   TRP E 164 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LEU E 166 " --> pdb=" O   LEU E 175 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   LEU E 175 " --> pdb=" O   LEU E 166 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 164 through 169

    469 hydrogen bonds defined for protein.
    1320 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.38

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2759
        1.34 -     1.46: 2106
        1.46 -     1.58: 3777
        1.58 -     1.70: 0
        1.70 -     1.81: 74
  Bond restraints: 8716
  Sorted by residual:
  bond pdb=" CA  GLU C 130 "
       pdb=" CB  GLU C 130 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.69e-02 3.50e+03 1.02e+00
  bond pdb=" CG1 ILE F  64 "
       pdb=" CD1 ILE F  64 "
    ideal  model  delta    sigma   weight residual
    1.513  1.479  0.034 3.90e-02 6.57e+02 7.81e-01
  bond pdb=" CB  ASP F  71 "
       pdb=" CG  ASP F  71 "
    ideal  model  delta    sigma   weight residual
    1.516  1.495  0.021 2.50e-02 1.60e+03 7.28e-01
  bond pdb=" CB  LYS A  11 "
       pdb=" CG  LYS A  11 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.17e-01
  bond pdb=" CA  ASN C 313 "
       pdb=" C   ASN C 313 "
    ideal  model  delta    sigma   weight residual
    1.524  1.533 -0.009 1.23e-02 6.61e+03 5.93e-01
  ... (remaining 8711 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 11558
        1.55 -     3.10: 257
        3.10 -     4.65: 44
        4.65 -     6.21: 13
        6.21 -     7.76: 5
  Bond angle restraints: 11877
  Sorted by residual:
  angle pdb=" C   ARG E 179 "
        pdb=" N   MET E 180 "
        pdb=" CA  MET E 180 "
      ideal   model   delta    sigma   weight residual
     121.54  128.88   -7.34 1.91e+00 2.74e-01 1.48e+01
  angle pdb=" CA  GLU C 130 "
        pdb=" CB  GLU C 130 "
        pdb=" CG  GLU C 130 "
      ideal   model   delta    sigma   weight residual
     114.10  121.06   -6.96 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" C   ARG C 129 "
        pdb=" N   GLU C 130 "
        pdb=" CA  GLU C 130 "
      ideal   model   delta    sigma   weight residual
     121.54  126.46   -4.92 1.91e+00 2.74e-01 6.63e+00
  angle pdb=" CB  LYS A  11 "
        pdb=" CG  LYS A  11 "
        pdb=" CD  LYS A  11 "
      ideal   model   delta    sigma   weight residual
     111.30  116.88   -5.58 2.30e+00 1.89e-01 5.88e+00
  angle pdb=" CA  LYS B  73 "
        pdb=" CB  LYS B  73 "
        pdb=" CG  LYS B  73 "
      ideal   model   delta    sigma   weight residual
     114.10  118.95   -4.85 2.00e+00 2.50e-01 5.87e+00
  ... (remaining 11872 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4611
       17.69 -    35.38: 390
       35.38 -    53.06: 69
       53.06 -    70.75: 10
       70.75 -    88.44: 5
  Dihedral angle restraints: 5085
    sinusoidal: 1795
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  LYS B  73 "
           pdb=" C   LYS B  73 "
           pdb=" N   PHE B  74 "
           pdb=" CA  PHE B  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.15   27.85     0      5.00e+00 4.00e-02 3.10e+01
  dihedral pdb=" CA  GLY B 181 "
           pdb=" C   GLY B 181 "
           pdb=" N   ASP B 182 "
           pdb=" CA  ASP B 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.46   16.54     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CB  GLU C 138 "
           pdb=" CG  GLU C 138 "
           pdb=" CD  GLU C 138 "
           pdb=" OE1 GLU C 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.44   88.44     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 5082 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 889
       0.032 -    0.064: 324
       0.064 -    0.095: 104
       0.095 -    0.127: 57
       0.127 -    0.159: 8
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  GLU C 130 "
            pdb=" N   GLU C 130 "
            pdb=" C   GLU C 130 "
            pdb=" CB  GLU C 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" CG  LEU F  72 "
            pdb=" CB  LEU F  72 "
            pdb=" CD1 LEU F  72 "
            pdb=" CD2 LEU F  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.59e-01
  chirality pdb=" CA  THR F  87 "
            pdb=" N   THR F  87 "
            pdb=" C   THR F  87 "
            pdb=" CB  THR F  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 1379 not shown)

  Planarity restraints: 1504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 332 "   -0.015 2.00e-02 2.50e+03   1.49e-02 5.54e+00
        pdb=" CG  TRP C 332 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 332 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 332 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 332 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 332 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 332 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 332 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 332 "   -0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 332 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A   3 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.79e+00
        pdb=" N   PRO A   4 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A   4 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A   4 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  69 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.45e+00
        pdb=" C   VAL F  69 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   VAL F  69 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ALA F  70 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1501 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 266
        2.71 -     3.26: 8531
        3.26 -     3.81: 14009
        3.81 -     4.35: 16871
        4.35 -     4.90: 28921
  Nonbonded interactions: 68598
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 161 "
            pdb=" OD1 ASP C 163 "
     model   vdw
     2.168 3.040
  nonbonded pdb=" O   GLN C  75 "
            pdb=" OG  SER C  98 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OG  SER C 281 "
            pdb=" O   HIS D  44 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" NZ  LYS B  95 "
            pdb=" OD2 ASP C 228 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   ALA B  41 "
            pdb=" OG  SER B  44 "
     model   vdw
     2.252 3.040
  ... (remaining 68593 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.360
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8716  Z= 0.160
  Angle     :  0.607   7.758  11877  Z= 0.327
  Chirality :  0.041   0.159   1382
  Planarity :  0.004   0.055   1504
  Dihedral  : 13.569  88.438   2957
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1115
  helix:  2.17 (0.26), residues: 401
  sheet:  0.49 (0.31), residues: 272
  loop : -1.04 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP C 332 
 HIS   0.008   0.001   HIS B  82 
 PHE   0.020   0.002   PHE B  74 
 TYR   0.013   0.001   TYR B 191 
 ARG   0.009   0.001   ARG B 185 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.8816 (t80) cc_final: 0.8449 (t80)
REVERT: B   73 LYS cc_start: 0.8376 (mmtm) cc_final: 0.7713 (pttm)
REVERT: B  122 LEU cc_start: 0.8967 (mt) cc_final: 0.8647 (mp)
REVERT: B  232 LYS cc_start: 0.8886 (tttp) cc_final: 0.8627 (tttp)
REVERT: C  289 TYR cc_start: 0.8566 (m-80) cc_final: 0.8236 (m-80)
REVERT: C  301 LYS cc_start: 0.8592 (mmpt) cc_final: 0.8138 (mmmt)
REVERT: E   96 CYS cc_start: 0.8086 (t) cc_final: 0.7407 (t)
REVERT: E   98 ARG cc_start: 0.8524 (ptm160) cc_final: 0.7856 (ptm160)
REVERT: E  190 ARG cc_start: 0.7929 (ptp-170) cc_final: 0.7514 (ptp90)
REVERT: E  192 SER cc_start: 0.7065 (t) cc_final: 0.6830 (t)
REVERT: E  218 MET cc_start: 0.7594 (tmm) cc_final: 0.6614 (tmm)
REVERT: F   55 GLN cc_start: 0.8187 (mp10) cc_final: 0.7974 (mp10)
REVERT: F  244 LEU cc_start: 0.8064 (tp) cc_final: 0.7850 (tt)
REVERT: F  305 THR cc_start: 0.7514 (m) cc_final: 0.7127 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.2037
  time to fit residues: 74.9618
Evaluate side-chains
  227 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 87 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 ASN
** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 182 ASN
** F  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 102 HIS
** F 252 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 = 0.3888 r_free = 0.3888 target = 0.153430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.113947 restraints weight = 12977.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.117950 restraints weight = 6956.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.120344 restraints weight = 4742.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.058   8716  Z= 0.520
  Angle     :  0.747  10.580  11877  Z= 0.393
  Chirality :  0.049   0.248   1382
  Planarity :  0.005   0.059   1504
  Dihedral  :  4.518  34.626   1222
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.53 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.25), residues: 1115
  helix:  1.71 (0.26), residues: 403
  sheet:  0.27 (0.31), residues: 273
  loop : -1.01 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 211 
 HIS   0.006   0.002   HIS C  91 
 PHE   0.022   0.003   PHE F 303 
 TYR   0.022   0.003   TYR F 163 
 ARG   0.006   0.001   ARG C 283 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 225
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9213 (t80) cc_final: 0.8414 (t80)
REVERT: B   73 LYS cc_start: 0.8754 (mmtm) cc_final: 0.7982 (pttm)
REVERT: C  101 MET cc_start: 0.8567 (mtm) cc_final: 0.8189 (ptp)
REVERT: C  118 ASP cc_start: 0.8064 (p0) cc_final: 0.7799 (p0)
REVERT: C  153 ASP cc_start: 0.7780 (m-30) cc_final: 0.7492 (m-30)
REVERT: C  264 TYR cc_start: 0.8438 (m-10) cc_final: 0.8158 (m-80)
REVERT: C  301 LYS cc_start: 0.8329 (mmpt) cc_final: 0.7965 (mmmt)
REVERT: E  143 VAL cc_start: 0.8342 (t) cc_final: 0.8099 (m)
REVERT: E  177 ILE cc_start: 0.8759 (tp) cc_final: 0.8511 (tp)
REVERT: E  180 MET cc_start: 0.7321 (ptt) cc_final: 0.6919 (ptt)
REVERT: E  190 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7551 (ptp90)
REVERT: E  218 MET cc_start: 0.8245 (tmm) cc_final: 0.7509 (tmm)
REVERT: E  219 GLN cc_start: 0.9035 (pp30) cc_final: 0.8357 (pp30)
REVERT: F   55 GLN cc_start: 0.8172 (mp10) cc_final: 0.7888 (mp10)
REVERT: F  114 PHE cc_start: 0.8543 (m-80) cc_final: 0.8340 (m-80)
REVERT: F  129 TYR cc_start: 0.8625 (m-10) cc_final: 0.8268 (m-10)
REVERT: F  172 LEU cc_start: 0.9053 (mt) cc_final: 0.8843 (mt)
REVERT: F  237 MET cc_start: 0.8574 (mmm) cc_final: 0.7856 (mmt)
  outliers start: 24
  outliers final: 19
  residues processed: 235
  average time/residue: 0.1931
  time to fit residues: 63.0236
Evaluate side-chains
  229 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 210
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  181 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain E residue  126 ILE
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  187 VAL
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  174 VAL
Chi-restraints excluded: chain F residue  185 ARG
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  275 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 93 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 96 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN
D  44 HIS
** F 252 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 = 0.3952 r_free = 0.3952 target = 0.159103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.120107 restraints weight = 12948.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.124425 restraints weight = 6744.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.127231 restraints weight = 4500.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8716  Z= 0.191
  Angle     :  0.592   9.359  11877  Z= 0.304
  Chirality :  0.043   0.148   1382
  Planarity :  0.004   0.049   1504
  Dihedral  :  4.333  32.351   1222
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.23 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1115
  helix:  2.17 (0.26), residues: 396
  sheet:  0.33 (0.32), residues: 265
  loop : -0.91 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 297 
 HIS   0.004   0.001   HIS C 311 
 PHE   0.029   0.002   PHE F 303 
 TYR   0.024   0.002   TYR F 164 
 ARG   0.005   0.000   ARG B 185 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9139 (t80) cc_final: 0.8571 (t80)
REVERT: B   73 LYS cc_start: 0.8677 (mmtm) cc_final: 0.7876 (pttm)
REVERT: B  122 LEU cc_start: 0.8847 (mp) cc_final: 0.8614 (mp)
REVERT: C  153 ASP cc_start: 0.7664 (m-30) cc_final: 0.7336 (m-30)
REVERT: C  219 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7921 (ttm110)
REVERT: C  264 TYR cc_start: 0.8501 (m-10) cc_final: 0.8188 (m-80)
REVERT: C  301 LYS cc_start: 0.8347 (mmpt) cc_final: 0.7941 (mmmt)
REVERT: E   98 ARG cc_start: 0.8285 (ptm160) cc_final: 0.7962 (ptm160)
REVERT: E  143 VAL cc_start: 0.8358 (t) cc_final: 0.8128 (m)
REVERT: E  180 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7035 (ptt)
REVERT: E  190 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7567 (ptp90)
REVERT: E  218 MET cc_start: 0.8178 (tmm) cc_final: 0.7852 (tmm)
REVERT: F   55 GLN cc_start: 0.8109 (mp10) cc_final: 0.7829 (mp10)
REVERT: F  114 PHE cc_start: 0.8387 (m-80) cc_final: 0.8108 (m-80)
REVERT: F  129 TYR cc_start: 0.8720 (m-10) cc_final: 0.8182 (m-10)
REVERT: F  237 MET cc_start: 0.8546 (mmm) cc_final: 0.8005 (mmt)
REVERT: F  275 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9100 (tp)
  outliers start: 26
  outliers final: 14
  residues processed: 247
  average time/residue: 0.1867
  time to fit residues: 64.9401
Evaluate side-chains
  242 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 226
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  275 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 86 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 63 optimal weight:    9.9990
   chunk 89 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
** F  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 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 = 0.3898 r_free = 0.3898 target = 0.154384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.115220 restraints weight = 12986.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.119270 restraints weight = 6884.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.121853 restraints weight = 4662.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8716  Z= 0.309
  Angle     :  0.628  13.469  11877  Z= 0.324
  Chirality :  0.044   0.174   1382
  Planarity :  0.004   0.053   1504
  Dihedral  :  4.477  33.342   1222
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.54 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1115
  helix:  2.11 (0.26), residues: 396
  sheet:  0.31 (0.32), residues: 265
  loop : -0.94 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 297 
 HIS   0.003   0.001   HIS C 311 
 PHE   0.031   0.002   PHE F 303 
 TYR   0.021   0.002   TYR F 213 
 ARG   0.004   0.001   ARG E  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 218
  time to evaluate  : 0.880 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9250 (t80) cc_final: 0.8679 (t80)
REVERT: B   73 LYS cc_start: 0.8759 (mmtm) cc_final: 0.7884 (pttm)
REVERT: B  122 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8716 (mp)
REVERT: B  185 ARG cc_start: 0.8038 (ptt-90) cc_final: 0.7827 (ptt-90)
REVERT: C  118 ASP cc_start: 0.8057 (p0) cc_final: 0.7779 (p0)
REVERT: C  153 ASP cc_start: 0.7829 (m-30) cc_final: 0.7514 (m-30)
REVERT: C  264 TYR cc_start: 0.8521 (m-10) cc_final: 0.8246 (m-80)
REVERT: C  301 LYS cc_start: 0.8392 (mmpt) cc_final: 0.7965 (mmmt)
REVERT: E   18 ARG cc_start: 0.6924 (tpt-90) cc_final: 0.6553 (tpt-90)
REVERT: E   98 ARG cc_start: 0.8239 (ptm160) cc_final: 0.7870 (ptm160)
REVERT: E  143 VAL cc_start: 0.8328 (t) cc_final: 0.8082 (m)
REVERT: E  177 ILE cc_start: 0.8648 (tp) cc_final: 0.8446 (tp)
REVERT: E  180 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7087 (ptt)
REVERT: E  218 MET cc_start: 0.8243 (tmm) cc_final: 0.7828 (tmm)
REVERT: E  219 GLN cc_start: 0.8948 (pp30) cc_final: 0.8568 (pp30)
REVERT: F  129 TYR cc_start: 0.8880 (m-10) cc_final: 0.8400 (m-10)
REVERT: F  237 MET cc_start: 0.8638 (mmm) cc_final: 0.8060 (mmt)
REVERT: F  275 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9130 (tp)
  outliers start: 29
  outliers final: 19
  residues processed: 234
  average time/residue: 0.1972
  time to fit residues: 64.1594
Evaluate side-chains
  238 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 216
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  160 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue    4 LEU
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  267 THR
Chi-restraints excluded: chain F residue  275 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 93 optimal weight:    0.7980
   chunk 74 optimal weight:   40.0000
   chunk 71 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 156 GLN
C 220 GLN
** F  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 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 = 0.3898 r_free = 0.3898 target = 0.154397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.115287 restraints weight = 12970.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.119360 restraints weight = 6871.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.121991 restraints weight = 4642.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8716  Z= 0.283
  Angle     :  0.620  17.199  11877  Z= 0.317
  Chirality :  0.044   0.147   1382
  Planarity :  0.004   0.046   1504
  Dihedral  :  4.495  35.887   1222
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 19.77 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1115
  helix:  2.15 (0.26), residues: 396
  sheet:  0.25 (0.32), residues: 266
  loop : -0.93 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 297 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.036   0.002   PHE F 303 
 TYR   0.026   0.002   TYR F 213 
 ARG   0.004   0.000   ARG C 219 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 221
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9223 (t80) cc_final: 0.8812 (t80)
REVERT: B   73 LYS cc_start: 0.8705 (mmtm) cc_final: 0.7928 (pttm)
REVERT: B  185 ARG cc_start: 0.7920 (ptt-90) cc_final: 0.7558 (ptt-90)
REVERT: C  153 ASP cc_start: 0.7742 (m-30) cc_final: 0.7422 (m-30)
REVERT: C  237 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7285 (p0)
REVERT: C  264 TYR cc_start: 0.8550 (m-10) cc_final: 0.8293 (m-80)
REVERT: C  301 LYS cc_start: 0.8403 (mmpt) cc_final: 0.8040 (mmmt)
REVERT: D   48 ASP cc_start: 0.8800 (t0) cc_final: 0.8588 (t0)
REVERT: E   18 ARG cc_start: 0.7069 (tpt-90) cc_final: 0.6718 (tpt-90)
REVERT: E   98 ARG cc_start: 0.8321 (ptm160) cc_final: 0.7942 (ptm160)
REVERT: E  143 VAL cc_start: 0.8348 (t) cc_final: 0.8109 (m)
REVERT: E  177 ILE cc_start: 0.8553 (tp) cc_final: 0.8199 (tp)
REVERT: E  180 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7186 (ptt)
REVERT: E  190 ARG cc_start: 0.7887 (ptp-170) cc_final: 0.7396 (ptp90)
REVERT: E  218 MET cc_start: 0.8280 (tmm) cc_final: 0.8057 (tmm)
REVERT: E  219 GLN cc_start: 0.8964 (pp30) cc_final: 0.8432 (pp30)
REVERT: F   55 GLN cc_start: 0.8024 (mp10) cc_final: 0.7818 (mp10)
REVERT: F  129 TYR cc_start: 0.8829 (m-80) cc_final: 0.8424 (m-10)
REVERT: F  237 MET cc_start: 0.8703 (mmm) cc_final: 0.8134 (mmt)
REVERT: F  275 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9152 (tp)
  outliers start: 40
  outliers final: 30
  residues processed: 240
  average time/residue: 0.1864
  time to fit residues: 62.8058
Evaluate side-chains
  247 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 214
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  156 GLN
Chi-restraints excluded: chain C residue  160 SER
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  312 ASP
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  275 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
D  44 HIS
** F  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 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 = 0.3929 r_free = 0.3929 target = 0.156982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.118325 restraints weight = 12829.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.122477 restraints weight = 6740.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.125107 restraints weight = 4522.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7680
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8716  Z= 0.199
  Angle     :  0.614  21.157  11877  Z= 0.306
  Chirality :  0.044   0.371   1382
  Planarity :  0.004   0.045   1504
  Dihedral  :  4.372  34.210   1222
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.73 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.25), residues: 1115
  helix:  2.26 (0.26), residues: 396
  sheet:  0.27 (0.32), residues: 278
  loop : -0.88 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 297 
 HIS   0.002   0.001   HIS B 209 
 PHE   0.030   0.002   PHE F 303 
 TYR   0.018   0.002   TYR F 196 
 ARG   0.004   0.000   ARG C 219 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 221
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9172 (t80) cc_final: 0.8779 (t80)
REVERT: B   73 LYS cc_start: 0.8648 (mmtm) cc_final: 0.7901 (pttm)
REVERT: B  185 ARG cc_start: 0.7925 (ptt-90) cc_final: 0.7645 (ptt-90)
REVERT: C  153 ASP cc_start: 0.7752 (m-30) cc_final: 0.7440 (m-30)
REVERT: C  237 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7182 (p0)
REVERT: C  264 TYR cc_start: 0.8550 (m-10) cc_final: 0.8320 (m-80)
REVERT: C  275 SER cc_start: 0.9231 (t) cc_final: 0.8869 (p)
REVERT: C  301 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8117 (mmmt)
REVERT: D   48 ASP cc_start: 0.8713 (t0) cc_final: 0.8498 (t70)
REVERT: E   18 ARG cc_start: 0.7102 (tpt-90) cc_final: 0.6743 (tpt-90)
REVERT: E   34 MET cc_start: 0.8209 (mmm) cc_final: 0.7806 (mmp)
REVERT: E   98 ARG cc_start: 0.8327 (ptm160) cc_final: 0.8000 (ptm160)
REVERT: E  143 VAL cc_start: 0.8343 (t) cc_final: 0.8103 (m)
REVERT: E  177 ILE cc_start: 0.8512 (tp) cc_final: 0.8133 (tp)
REVERT: E  180 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7130 (ptt)
REVERT: E  190 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.7350 (ptp90)
REVERT: E  218 MET cc_start: 0.8250 (tmm) cc_final: 0.7996 (tmm)
REVERT: F   55 GLN cc_start: 0.8015 (mp10) cc_final: 0.7800 (mp10)
REVERT: F  114 PHE cc_start: 0.8658 (m-80) cc_final: 0.8263 (m-80)
REVERT: F  129 TYR cc_start: 0.8830 (m-80) cc_final: 0.8445 (m-10)
REVERT: F  156 PHE cc_start: 0.8968 (m-80) cc_final: 0.8613 (m-80)
REVERT: F  176 HIS cc_start: 0.7685 (p90) cc_final: 0.7352 (p-80)
REVERT: F  237 MET cc_start: 0.8660 (mmm) cc_final: 0.8159 (mmt)
REVERT: F  260 TRP cc_start: 0.7963 (m100) cc_final: 0.7672 (m100)
REVERT: F  275 ILE cc_start: 0.9471 (mm) cc_final: 0.9121 (tp)
  outliers start: 30
  outliers final: 23
  residues processed: 235
  average time/residue: 0.1840
  time to fit residues: 60.7712
Evaluate side-chains
  240 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 215
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  160 SER
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   37 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  286 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0170
   chunk 30 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 107 optimal weight:    0.3980
   chunk 64 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   overall best weight:    1.4824

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

Flipped N/Q/H residues before XYZ refinement:
** A   5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
** F  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 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 = 0.3920 r_free = 0.3920 target = 0.156210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.117090 restraints weight = 12889.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.121236 restraints weight = 6832.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.123901 restraints weight = 4601.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8716  Z= 0.237
  Angle     :  0.620  16.852  11877  Z= 0.311
  Chirality :  0.043   0.168   1382
  Planarity :  0.004   0.045   1504
  Dihedral  :  4.345  34.841   1222
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 22.20 %
    Favored  : 74.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1115
  helix:  2.24 (0.26), residues: 396
  sheet:  0.31 (0.32), residues: 276
  loop : -0.90 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 297 
 HIS   0.003   0.001   HIS B 209 
 PHE   0.027   0.002   PHE F 303 
 TYR   0.022   0.002   TYR F 213 
 ARG   0.004   0.000   ARG B 117 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 226
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9195 (t80) cc_final: 0.8776 (t80)
REVERT: B   73 LYS cc_start: 0.8682 (mmtm) cc_final: 0.7910 (pttm)
REVERT: B  185 ARG cc_start: 0.7895 (ptt-90) cc_final: 0.7608 (ptt-90)
REVERT: C  153 ASP cc_start: 0.7683 (m-30) cc_final: 0.7423 (m-30)
REVERT: C  237 ASN cc_start: 0.7509 (OUTLIER) cc_final: 0.7262 (p0)
REVERT: C  264 TYR cc_start: 0.8483 (m-10) cc_final: 0.8249 (m-80)
REVERT: C  275 SER cc_start: 0.9227 (t) cc_final: 0.8759 (p)
REVERT: C  301 LYS cc_start: 0.8387 (mmpt) cc_final: 0.8102 (mmmt)
REVERT: D   48 ASP cc_start: 0.8696 (t0) cc_final: 0.8343 (t70)
REVERT: E   98 ARG cc_start: 0.8298 (ptm160) cc_final: 0.7977 (ptm160)
REVERT: E  143 VAL cc_start: 0.8368 (t) cc_final: 0.8129 (m)
REVERT: E  177 ILE cc_start: 0.8510 (tp) cc_final: 0.8108 (tp)
REVERT: E  180 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7212 (ptt)
REVERT: E  190 ARG cc_start: 0.7848 (ptp-170) cc_final: 0.7295 (ptp90)
REVERT: E  219 GLN cc_start: 0.8907 (pp30) cc_final: 0.8522 (pp30)
REVERT: F  114 PHE cc_start: 0.8691 (m-80) cc_final: 0.8273 (m-80)
REVERT: F  129 TYR cc_start: 0.8877 (m-80) cc_final: 0.8474 (m-10)
REVERT: F  237 MET cc_start: 0.8670 (mmm) cc_final: 0.8167 (mmt)
REVERT: F  260 TRP cc_start: 0.7968 (m100) cc_final: 0.7634 (m100)
REVERT: F  275 ILE cc_start: 0.9477 (mm) cc_final: 0.9132 (tp)
  outliers start: 31
  outliers final: 24
  residues processed: 239
  average time/residue: 0.1848
  time to fit residues: 62.0531
Evaluate side-chains
  244 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 218
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  200 VAL
Chi-restraints excluded: chain F residue  241 VAL
Chi-restraints excluded: chain F residue  286 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0470
   chunk 4 optimal weight:    0.6980
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7278

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
C 313 ASN
C 340 ASN
** F 252 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 = 0.3952 r_free = 0.3952 target = 0.158716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.119631 restraints weight = 13078.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.123761 restraints weight = 6847.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.126635 restraints weight = 4611.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8716  Z= 0.186
  Angle     :  0.610  17.717  11877  Z= 0.305
  Chirality :  0.042   0.155   1382
  Planarity :  0.004   0.044   1504
  Dihedral  :  4.237  31.757   1222
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 23.01 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1115
  helix:  2.34 (0.26), residues: 393
  sheet:  0.30 (0.32), residues: 278
  loop : -0.85 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 297 
 HIS   0.002   0.001   HIS F 102 
 PHE   0.025   0.002   PHE E  27 
 TYR   0.023   0.002   TYR F 164 
 ARG   0.004   0.000   ARG E  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 228
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9142 (t80) cc_final: 0.8714 (t80)
REVERT: B   73 LYS cc_start: 0.8629 (mmtm) cc_final: 0.7802 (pttm)
REVERT: C  153 ASP cc_start: 0.7763 (m-30) cc_final: 0.7394 (m-30)
REVERT: C  237 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.7212 (p0)
REVERT: C  275 SER cc_start: 0.9200 (t) cc_final: 0.8754 (p)
REVERT: C  301 LYS cc_start: 0.8357 (mmpt) cc_final: 0.8099 (mmmt)
REVERT: D   48 ASP cc_start: 0.8777 (t0) cc_final: 0.8407 (t70)
REVERT: E   18 ARG cc_start: 0.6773 (tpt-90) cc_final: 0.6517 (tpt-90)
REVERT: E  143 VAL cc_start: 0.8390 (t) cc_final: 0.8156 (m)
REVERT: E  177 ILE cc_start: 0.8476 (tp) cc_final: 0.8066 (tp)
REVERT: E  180 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7107 (ptt)
REVERT: E  190 ARG cc_start: 0.7897 (ptp-170) cc_final: 0.7368 (ptp90)
REVERT: E  219 GLN cc_start: 0.8994 (pp30) cc_final: 0.8607 (pp30)
REVERT: F  114 PHE cc_start: 0.8590 (m-80) cc_final: 0.8261 (m-80)
REVERT: F  129 TYR cc_start: 0.8783 (m-80) cc_final: 0.8437 (m-10)
REVERT: F  176 HIS cc_start: 0.7676 (p90) cc_final: 0.7409 (p-80)
REVERT: F  237 MET cc_start: 0.8625 (mmm) cc_final: 0.8133 (mmt)
REVERT: F  260 TRP cc_start: 0.7983 (m100) cc_final: 0.7679 (m100)
REVERT: F  275 ILE cc_start: 0.9449 (mm) cc_final: 0.9121 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 240
  average time/residue: 0.1856
  time to fit residues: 62.5219
Evaluate side-chains
  242 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  195 LYS
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  286 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 89 optimal weight:    0.4980
   chunk 7 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 6 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 76 optimal weight:    7.9990
   chunk 70 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.157052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.117693 restraints weight = 12993.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.121867 restraints weight = 6891.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124658 restraints weight = 4655.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8716  Z= 0.235
  Angle     :  0.630  16.030  11877  Z= 0.316
  Chirality :  0.043   0.154   1382
  Planarity :  0.004   0.043   1504
  Dihedral  :  4.289  32.426   1222
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.58 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.25), residues: 1115
  helix:  2.30 (0.26), residues: 394
  sheet:  0.28 (0.32), residues: 280
  loop : -0.87 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 297 
 HIS   0.002   0.001   HIS B 209 
 PHE   0.024   0.002   PHE F 303 
 TYR   0.020   0.002   TYR F 213 
 ARG   0.007   0.000   ARG B 185 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 224
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9196 (t80) cc_final: 0.8748 (t80)
REVERT: B   73 LYS cc_start: 0.8767 (mmtm) cc_final: 0.7858 (pttm)
REVERT: B  166 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8262 (mm-30)
REVERT: B  185 ARG cc_start: 0.8022 (ptt-90) cc_final: 0.7802 (ptt-90)
REVERT: C  153 ASP cc_start: 0.7763 (m-30) cc_final: 0.7379 (m-30)
REVERT: C  237 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7216 (p0)
REVERT: C  275 SER cc_start: 0.9228 (t) cc_final: 0.8755 (p)
REVERT: C  301 LYS cc_start: 0.8390 (mmpt) cc_final: 0.8143 (mmmt)
REVERT: D   48 ASP cc_start: 0.8813 (t0) cc_final: 0.8406 (t70)
REVERT: E   18 ARG cc_start: 0.6873 (tpt-90) cc_final: 0.6624 (tpt-90)
REVERT: E  177 ILE cc_start: 0.8406 (tp) cc_final: 0.8000 (tp)
REVERT: E  180 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7105 (ptt)
REVERT: E  190 ARG cc_start: 0.7894 (ptp-170) cc_final: 0.7334 (ptp90)
REVERT: F  114 PHE cc_start: 0.8671 (m-80) cc_final: 0.8239 (m-80)
REVERT: F  129 TYR cc_start: 0.8804 (m-80) cc_final: 0.8432 (m-10)
REVERT: F  176 HIS cc_start: 0.7721 (p90) cc_final: 0.7430 (p-80)
REVERT: F  237 MET cc_start: 0.8653 (mmm) cc_final: 0.8094 (mmt)
REVERT: F  260 TRP cc_start: 0.8075 (m100) cc_final: 0.7537 (m100)
REVERT: F  275 ILE cc_start: 0.9451 (mm) cc_final: 0.9113 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 233
  average time/residue: 0.1967
  time to fit residues: 63.7200
Evaluate side-chains
  244 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 221
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain C residue   76 ASP
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  277 SER
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  145 ILE
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  286 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 174 GLN
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 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 = 0.3941 r_free = 0.3941 target = 0.157868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.118957 restraints weight = 12947.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.123184 restraints weight = 6807.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.125972 restraints weight = 4562.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8716  Z= 0.210
  Angle     :  0.629  15.923  11877  Z= 0.315
  Chirality :  0.043   0.155   1382
  Planarity :  0.004   0.043   1504
  Dihedral  :  4.262  31.922   1222
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 24.16 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.25), residues: 1115
  helix:  2.26 (0.26), residues: 394
  sheet:  0.27 (0.32), residues: 277
  loop : -0.85 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 297 
 HIS   0.002   0.001   HIS F 110 
 PHE   0.025   0.002   PHE F 303 
 TYR   0.022   0.002   TYR F 213 
 ARG   0.007   0.000   ARG B 185 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 227
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 TYR cc_start: 0.9170 (t80) cc_final: 0.8747 (t80)
REVERT: B   73 LYS cc_start: 0.8727 (mmtm) cc_final: 0.7837 (pttm)
REVERT: C  153 ASP cc_start: 0.7701 (m-30) cc_final: 0.7324 (m-30)
REVERT: C  237 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7278 (p0)
REVERT: C  275 SER cc_start: 0.9215 (t) cc_final: 0.8739 (p)
REVERT: C  301 LYS cc_start: 0.8391 (mmpt) cc_final: 0.8170 (mmmt)
REVERT: C  332 TRP cc_start: 0.8519 (m-10) cc_final: 0.8300 (m-10)
REVERT: D   48 ASP cc_start: 0.8780 (t0) cc_final: 0.8376 (t70)
REVERT: E  148 ARG cc_start: 0.8122 (mmt180) cc_final: 0.6873 (mtm110)
REVERT: E  177 ILE cc_start: 0.8436 (tp) cc_final: 0.8022 (tp)
REVERT: E  180 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7093 (ptt)
REVERT: E  190 ARG cc_start: 0.7887 (ptp-170) cc_final: 0.7333 (ptp90)
REVERT: E  219 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8494 (tm-30)
REVERT: F  114 PHE cc_start: 0.8602 (m-80) cc_final: 0.8277 (m-80)
REVERT: F  129 TYR cc_start: 0.8739 (m-80) cc_final: 0.8446 (m-10)
REVERT: F  176 HIS cc_start: 0.7617 (p90) cc_final: 0.7330 (p-80)
REVERT: F  237 MET cc_start: 0.8650 (mmm) cc_final: 0.8052 (mmt)
REVERT: F  260 TRP cc_start: 0.8053 (m100) cc_final: 0.7564 (m100)
REVERT: F  275 ILE cc_start: 0.9463 (mm) cc_final: 0.9121 (tp)
  outliers start: 23
  outliers final: 18
  residues processed: 236
  average time/residue: 0.1961
  time to fit residues: 64.4006
Evaluate side-chains
  245 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 225
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain C residue   84 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  237 ASN
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain E residue   74 ASP
Chi-restraints excluded: chain E residue  127 VAL
Chi-restraints excluded: chain E residue  160 THR
Chi-restraints excluded: chain E residue  162 LEU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   57 VAL
Chi-restraints excluded: chain F residue   88 LEU
Chi-restraints excluded: chain F residue  105 ILE
Chi-restraints excluded: chain F residue  286 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 97 optimal weight:    0.1980
   chunk 39 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 74 optimal weight:   40.0000
   chunk 47 optimal weight:    2.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 220 GLN
** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 252 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 = 0.3916 r_free = 0.3916 target = 0.155818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116647 restraints weight = 13131.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.120801 restraints weight = 6897.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.123481 restraints weight = 4620.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8716  Z= 0.269
  Angle     :  0.651  15.827  11877  Z= 0.327
  Chirality :  0.043   0.163   1382
  Planarity :  0.004   0.043   1504
  Dihedral  :  4.339  33.659   1222
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.05 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1115
  helix:  2.20 (0.26), residues: 395
  sheet:  0.26 (0.31), residues: 279
  loop : -0.86 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP C 297 
 HIS   0.002   0.001   HIS C  91 
 PHE   0.024   0.002   PHE F 303 
 TYR   0.023   0.002   TYR F 213 
 ARG   0.011   0.001   ARG B 132 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3123.87 seconds
wall clock time: 54 minutes 55.27 seconds (3295.27 seconds total)