Starting phenix.real_space_refine
on Fri Aug 22 18:34:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8idb_35362/08_2025/8idb_35362.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8idb_35362/08_2025/8idb_35362.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8idb_35362/08_2025/8idb_35362.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8idb_35362/08_2025/8idb_35362.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8idb_35362/08_2025/8idb_35362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8idb_35362/08_2025/8idb_35362.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.027
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      27      5.16       5
     C    4337      2.51       5
     N    1208      2.21       5
     O    1263      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6835
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1421
          Classifications: {'peptide': 205}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 8, 'TRANS': 196}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 190
          Unresolved non-hydrogen angles: 228
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 11, 'ASP:plan': 7, 'GLU:plan': 5, 'PHE:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 119
    Chain: "B"
      Number of atoms: 1280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1280
          Classifications: {'peptide': 197}
          Incomplete info: {'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 8, 'TRANS': 188}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 270
          Unresolved non-hydrogen angles: 331
          Unresolved non-hydrogen dihedrals: 219
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'GLU:plan': 9, 'PHE:plan': 3, 'ARG:plan': 9, 'HIS:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 149
    Chain: "C"
      Number of atoms: 2078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2078
          Classifications: {'peptide': 285}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 5, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 130
          Unresolved non-hydrogen angles: 161
          Unresolved non-hydrogen dihedrals: 109
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 77
    Chain: "D"
      Number of atoms: 2056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2056
          Classifications: {'peptide': 295}
          Incomplete info: {'truncation_to_alanine': 56}
          Link IDs: {'PTRANS': 6, 'TRANS': 288}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 239
          Unresolved non-hydrogen angles: 300
          Unresolved non-hydrogen dihedrals: 203
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 6, 'ASP:plan': 6, 'GLU:plan': 5, 'TYR:plan': 4, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 145
  Time building chain proxies: 1.31, per 1000 atoms: 0.19
  Number of scatterers: 6835
  At special positions: 0
  Unit cell: (90.1, 99.64, 138.86, 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      27     16.00
     O    1263      8.00
     N    1208      7.00
     C    4337      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  73 " - pdb=" SG  CYS D  78 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 300.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      53.4% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 4.281A  pdb=" N   LEU A  50 " --> pdb=" O   MET A  47 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU A  51 " --> pdb=" O   ARG A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 47 through 51'
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 3.563A  pdb=" N   LEU A  79 " --> pdb=" O   HIS A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 102
      removed outlier: 3.610A  pdb=" N   VAL A 102 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 110
      removed outlier: 3.973A  pdb=" N   ILE A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 142 through 154
      removed outlier: 4.402A  pdb=" N   GLN A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ARG A 147 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 174
    Processing helix  chain 'A' and resid 175 through 184
      removed outlier: 3.911A  pdb=" N   MET A 179 " --> pdb=" O   SER A 175 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ARG A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 189
      removed outlier: 3.583A  pdb=" N   GLY A 189 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 4.198A  pdb=" N   MET A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 49
      removed outlier: 3.730A  pdb=" N   THR B  45 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   PHE B  46 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   MET B  47 " --> pdb=" O   LYS B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 84
      removed outlier: 3.563A  pdb=" N   LEU B  79 " --> pdb=" O   HIS B  75 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN B  81 " --> pdb=" O   PRO B  77 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   VAL B  82 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE B  83 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLY B  84 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 108
      removed outlier: 4.645A  pdb=" N   ALA B 105 " --> pdb=" O   ASN B 101 " (cutoff:3.500A)
      removed outlier: 5.609A  pdb=" N   LEU B 106 " --> pdb=" O   VAL B 102 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   GLU B 107 " --> pdb=" O   ALA B 103 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   VAL B 108 " --> pdb=" O   PHE B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.601A  pdb=" N   ASN B 117 " --> pdb=" O   THR B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 126
      removed outlier: 4.359A  pdb=" N   LEU B 124 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'B' and resid 146 through 154
      removed outlier: 3.616A  pdb=" N   PHE B 154 " --> pdb=" O   ILE B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 186
      removed outlier: 3.624A  pdb=" N   ASN B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 189
      No H-bonds generated for 'chain 'B' and resid 187 through 189'
    Processing helix  chain 'C' and resid 10 through 17
      removed outlier: 3.806A  pdb=" N   PHE C  14 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 27 through 49
      removed outlier: 3.917A  pdb=" N   SER C  31 " --> pdb=" O   THR C  27 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   PHE C  35 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 84
      removed outlier: 3.856A  pdb=" N   ALA C  80 " --> pdb=" O   THR C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 136 through 141
    Processing helix  chain 'C' and resid 164 through 198
      removed outlier: 3.893A  pdb=" N   GLN C 180 " --> pdb=" O   VAL C 176 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ILE C 182 " --> pdb=" O   LEU C 178 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   GLY C 183 " --> pdb=" O   VAL C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 209
      removed outlier: 3.851A  pdb=" N   ILE C 203 " --> pdb=" O   ARG C 199 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET C 206 " --> pdb=" O   GLU C 202 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 245
      removed outlier: 3.777A  pdb=" N   GLN C 217 " --> pdb=" O   ARG C 213 " (cutoff:3.500A)
      Proline residue:  C 219  - end of helix
      removed outlier: 3.570A  pdb=" N   ARG C 243 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 257
      removed outlier: 4.696A  pdb=" N   LEU C 251 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ASN C 252 " --> pdb=" O   GLU C 248 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   GLN C 253 " --> pdb=" O   ASN C 249 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE C 254 " --> pdb=" O   ALA C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 292
      removed outlier: 3.742A  pdb=" N   LEU C 269 " --> pdb=" O   TYR C 265 " (cutoff:3.500A)
      Proline residue:  C 273  - end of helix
      removed outlier: 4.014A  pdb=" N   THR C 290 " --> pdb=" O   THR C 286 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 17
      removed outlier: 4.114A  pdb=" N   VAL D  10 " --> pdb=" O   LEU D   6 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   LEU D  11 " --> pdb=" O   LEU D   7 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   THR D  12 " --> pdb=" O   ASN D   8 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE D  14 " --> pdb=" O   VAL D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 46
      removed outlier: 4.067A  pdb=" N   ILE D  22 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ILE D  30 " --> pdb=" O   LEU D  26 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   PHE D  35 " --> pdb=" O   SER D  31 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL D  41 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   VAL D  42 " --> pdb=" O   GLY D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 50
      removed outlier: 3.998A  pdb=" N   ALA D  50 " --> pdb=" O   SER D  47 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 47 through 50'
    Processing helix  chain 'D' and resid 63 through 68
      removed outlier: 3.926A  pdb=" N   SER D  67 " --> pdb=" O   THR D  63 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 75 through 88
      removed outlier: 4.436A  pdb=" N   LYS D  79 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR D  87 " --> pdb=" O   GLU D  83 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG D  88 " --> pdb=" O   LYS D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 114
      removed outlier: 3.753A  pdb=" N   LYS D 114 " --> pdb=" O   PRO D 111 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 132 through 134
      No H-bonds generated for 'chain 'D' and resid 132 through 134'
    Processing helix  chain 'D' and resid 135 through 144
    Processing helix  chain 'D' and resid 159 through 169
      removed outlier: 4.378A  pdb=" N   PHE D 163 " --> pdb=" O   ILE D 159 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU D 169 " --> pdb=" O   VAL D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 199
      removed outlier: 3.660A  pdb=" N   PHE D 174 " --> pdb=" O   SER D 170 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   ALA D 175 " --> pdb=" O   ASN D 171 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN D 180 " --> pdb=" O   VAL D 176 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ILE D 182 " --> pdb=" O   LEU D 178 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLY D 183 " --> pdb=" O   VAL D 179 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE D 188 " --> pdb=" O   ALA D 184 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA D 189 " --> pdb=" O   ILE D 185 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN D 190 " --> pdb=" O   LEU D 186 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL D 192 " --> pdb=" O   ILE D 188 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN D 193 " --> pdb=" O   ALA D 189 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 200 through 210
    Processing helix  chain 'D' and resid 217 through 247
      removed outlier: 3.690A  pdb=" N   ALA D 227 " --> pdb=" O   GLU D 223 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 247 through 257
      removed outlier: 5.386A  pdb=" N   GLN D 253 " --> pdb=" O   ASN D 249 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   PHE D 254 " --> pdb=" O   ALA D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 295
      removed outlier: 4.290A  pdb=" N   LEU D 277 " --> pdb=" O   PRO D 273 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LEU D 278 " --> pdb=" O   TRP D 274 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET D 282 " --> pdb=" O   LEU D 278 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   SER D 283 " --> pdb=" O   GLY D 279 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   THR D 286 " --> pdb=" O   MET D 282 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA D 287 " --> pdb=" O   SER D 283 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   ARG D 292 " --> pdb=" O   TYR D 288 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5
      removed outlier: 3.923A  pdb=" N   ILE A   3 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A  25 " --> pdb=" O   LEU A   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86
      removed outlier: 3.662A  pdb=" N   ASP A 164 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LEU A 161 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   ALA A 195 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ALA A 163 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 86
      removed outlier: 3.691A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   LEU B 161 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94
      removed outlier: 7.520A  pdb=" N   LYS C 129 " --> pdb=" O   LYS C  92 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 62
      removed outlier: 6.454A  pdb=" N   GLN D  59 " --> pdb=" O   VAL D 152 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   VAL D 152 " --> pdb=" O   GLN D  59 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   PHE D  61 " --> pdb=" O   LEU D 150 " (cutoff:3.500A)

    276 hydrogen bonds defined for protein.
    807 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: 0.85

  Time building geometry restraints manager: 0.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2314
        1.34 -     1.46: 1317
        1.46 -     1.58: 3240
        1.58 -     1.70: 0
        1.70 -     1.82: 50
  Bond restraints: 6921
  Sorted by residual:
  bond pdb=" CA  GLU A 165 "
       pdb=" CB  GLU A 165 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 8.30e-03 1.45e+04 5.81e+00
  bond pdb=" CG1 ILE C 188 "
       pdb=" CD1 ILE C 188 "
    ideal  model  delta    sigma   weight residual
    1.513  1.432  0.081 3.90e-02 6.57e+02 4.32e+00
  bond pdb=" C   VAL A  76 "
       pdb=" N   PRO A  77 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.23e-02 6.61e+03 3.46e+00
  bond pdb=" CB  MET D 191 "
       pdb=" CG  MET D 191 "
    ideal  model  delta    sigma   weight residual
    1.520  1.466  0.054 3.00e-02 1.11e+03 3.18e+00
  bond pdb=" C   VAL A 120 "
       pdb=" N   PRO A 121 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.016 9.40e-03 1.13e+04 2.87e+00
  ... (remaining 6916 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 9147
        2.55 -     5.10: 234
        5.10 -     7.66: 55
        7.66 -    10.21: 16
       10.21 -    12.76: 2
  Bond angle restraints: 9454
  Sorted by residual:
  angle pdb=" N   PRO D 273 "
        pdb=" CA  PRO D 273 "
        pdb=" C   PRO D 273 "
      ideal   model   delta    sigma   weight residual
     113.40  105.64    7.76 1.34e+00 5.57e-01 3.36e+01
  angle pdb=" C   ASP A 164 "
        pdb=" N   GLU A 165 "
        pdb=" CA  GLU A 165 "
      ideal   model   delta    sigma   weight residual
     124.21  130.24   -6.03 1.21e+00 6.83e-01 2.48e+01
  angle pdb=" C   ASP A  89 "
        pdb=" N   PHE A  90 "
        pdb=" CA  PHE A  90 "
      ideal   model   delta    sigma   weight residual
     121.54  130.95   -9.41 1.91e+00 2.74e-01 2.43e+01
  angle pdb=" C   HIS B  67 "
        pdb=" N   VAL B  68 "
        pdb=" CA  VAL B  68 "
      ideal   model   delta    sigma   weight residual
     121.97  130.23   -8.26 1.80e+00 3.09e-01 2.11e+01
  angle pdb=" C   TYR D 103 "
        pdb=" N   ASP D 104 "
        pdb=" CA  ASP D 104 "
      ideal   model   delta    sigma   weight residual
     121.54  129.71   -8.17 1.91e+00 2.74e-01 1.83e+01
  ... (remaining 9449 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 3873
       17.60 -    35.19: 211
       35.19 -    52.79: 32
       52.79 -    70.39: 5
       70.39 -    87.98: 4
  Dihedral angle restraints: 4125
    sinusoidal: 1294
      harmonic: 2831
  Sorted by residual:
  dihedral pdb=" CA  VAL D  56 "
           pdb=" C   VAL D  56 "
           pdb=" N   GLU D  57 "
           pdb=" CA  GLU D  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.87   26.13     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  ASP D  54 "
           pdb=" C   ASP D  54 "
           pdb=" N   ARG D  55 "
           pdb=" CA  ARG D  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.40  -22.60     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  ASN C  17 "
           pdb=" C   ASN C  17 "
           pdb=" N   VAL C  18 "
           pdb=" CA  VAL C  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.23   21.77     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 4122 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 937
       0.060 -    0.120: 205
       0.120 -    0.180: 47
       0.180 -    0.240: 11
       0.240 -    0.299: 3
  Chirality restraints: 1203
  Sorted by residual:
  chirality pdb=" CB  VAL C  32 "
            pdb=" CA  VAL C  32 "
            pdb=" CG1 VAL C  32 "
            pdb=" CG2 VAL C  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  MET C  20 "
            pdb=" N   MET C  20 "
            pdb=" C   MET C  20 "
            pdb=" CB  MET C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CB  ILE C 185 "
            pdb=" CA  ILE C 185 "
            pdb=" CG1 ILE C 185 "
            pdb=" CG2 ILE C 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.58e+00
  ... (remaining 1200 not shown)

  Planarity restraints: 1222
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 272 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   THR D 272 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   THR D 272 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PRO D 273 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  87 "    0.017 2.00e-02 2.50e+03   1.82e-02 5.79e+00
        pdb=" CG  PHE A  87 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  87 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  87 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  87 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  87 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  87 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 157 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.59e+00
        pdb=" CD  GLU C 157 "    0.041 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 157 "   -0.015 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 157 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1219 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1628
        2.78 -     3.31: 6491
        3.31 -     3.84: 10801
        3.84 -     4.37: 11477
        4.37 -     4.90: 19682
  Nonbonded interactions: 50079
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 171 "
            pdb=" OG1 THR A 174 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   GLY A  42 "
            pdb=" OG1 THR A  45 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   ILE C 268 "
            pdb=" OG1 THR C 272 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   GLU C  64 "
            pdb=" OG  SER C  67 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   ILE A 185 "
            pdb=" OG1 THR A 188 "
     model   vdw
     2.313 3.040
  ... (remaining 50074 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 8 or (resid 9 through 11 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 12 through 26 or (resid 27 through 29 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 30 through 35 or (resid \ 
 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 
 42 or (resid 43 and (name N or name CA or name C or name O or name CB )) or res \ 
id 44 through 54 or resid 64 through 66 or (resid 67 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 68 through 70 or (resid 71 through 72 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 73 through 80 or  \ 
(resid 81 and (name N or name CA or name C or name O or name CB )) or resid 82 t \ 
hrough 89 or (resid 90 through 92 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 93 through 95 or (resid 96 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 97 through 99 or (resid 100 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 and \ 
 (name N or name CA or name C or name O or name CB )) or (resid 110 through 115  \ 
and (name N or name CA or name C or name O or name CB )) or resid 116 or (resid  \ 
117 through 118 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 119 through 121 or (resid 122 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 123 through 124 or (resid 125 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 126 through 131 or (resid 132 through 140 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 141 through 143 or \ 
 (resid 144 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 
5 through 153 or (resid 154 and (name N or name CA or name C or name O or name C \ 
B )) or resid 155 through 158 or (resid 159 through 160 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 thro \ 
ugh 183 and (name N or name CA or name C or name O or name CB )) or resid 184 th \ 
rough 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 188 through 191 or (resid 192 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 193 through 213))
  selection = (chain 'B' and (resid 8 through 16 or (resid 17 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 18 through 19 or (resid 20 through 23 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 24 through 65 or (resi \ 
d 66 through 67 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 68 through 78 or (resid 79 through 81 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 82 through 88 or (resid 89 through 92 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 93 through 133 or (resid 134 t \ 
hrough 140 and (name N or name CA or name C or name O or name CB )) or resid 141 \ 
 through 202 or (resid 203 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 204 through 205 or (resid 206 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 207 or (resid 208 and (name N or name CA or name C  \ 
or name O or name CB )) or resid 209 through 213))
}
ncs_group {
  reference = (chain 'C' and (resid 4 through 6 or (resid 7 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 8 through 10 or (resid 11 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 12 through 14 or (resid 15 through 1 \ 
6 and (name N or name CA or name C or name O or name CB )) or resid 17 through 8 \ 
5 or (resid 86 through 87 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 88 through 109 or (resid 110 through 117 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 118 through 136 or (resid 137 through 138 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 139 through 1 \ 
40 or (resid 141 through 142 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 143 through 156 or (resid 157 through 158 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 159 through 166 or (resid 167 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 168 through 177 or (r \ 
esid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 t \ 
hrough 187 or (resid 188 through 189 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 190 through 191 or (resid 192 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 193 through 197 or (resid 198 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 199 or (resid 200 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 201 or (resid 202 thr \ 
ough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 o \ 
r (resid 205 through 208 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 209 through 214 or (resid 215 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA  \ 
or name C or name O or name CB )) or resid 219 or (resid 220 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 221 through 222 or (resid 223 thr \ 
ough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 t \ 
hrough 229 or (resid 230 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 231 through 242 or (resid 243 through 246 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 247 through 255 or (resid 256 through 257 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 258 through 2 \ 
69 or (resid 270 and (name N or name CA or name C or name O or name CB )) or res \ 
id 271 through 287 or (resid 288 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 289 through 294))
  selection = (chain 'D' and (resid 4 through 58 or (resid 59 through 60 and (name N or name C \ 
A or name C or name O or name CB )) or resid 61 or (resid 62 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 63 or (resid 64 through 65 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 66 through 68 or (re \ 
sid 69 through 70 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 71 through 72 or (resid 73 through 74 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 75 through 77 or (resid 78 through 80 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 81 through 82 or (resid 83 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 84 through 143  \ 
or (resid 144 and (name N or name CA or name C or name O or name CB )) or resid  \ 
145 or (resid 152 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 153 through 155 or (resid 156 through 158 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 159 through 212 or (resid 213 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 214 through 245 or (resid 246 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 247 through 294) \ 
)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.580
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.210
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
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      :  0.005   0.081   6922  Z= 0.225
  Angle     :  1.036  12.762   9456  Z= 0.534
  Chirality :  0.058   0.299   1203
  Planarity :  0.006   0.055   1222
  Dihedral  : 11.652  87.982   2280
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  5.79 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  1.13 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.59 (0.22), residues: 968
  helix: -2.26 (0.20), residues: 433
  sheet: -2.07 (0.91), residues: 39
  loop : -2.52 (0.23), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 118 
 TYR   0.025   0.002   TYR C 288 
 PHE   0.042   0.002   PHE A  87 
 TRP   0.008   0.001   TRP D 274 
 HIS   0.002   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 6921)
  covalent geometry    : angle       1.03562 ( 9454)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.44921 (    2)
  hydrogen bonds       : bond        0.18153 (  276)
  hydrogen bonds       : angle       7.03972 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   90 PHE cc_start: 0.8324 (m-80) cc_final: 0.8043 (m-80)
REVERT: B   34 PHE cc_start: 0.8126 (p90) cc_final: 0.7885 (p90)
REVERT: C   24 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7755 (tmm)
REVERT: C  249 ASN cc_start: 0.8130 (p0) cc_final: 0.7776 (p0)
REVERT: D   52 TYR cc_start: 0.8237 (m-80) cc_final: 0.8007 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0584
  time to fit residues: 11.7444
Evaluate side-chains
  114 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   24 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 GLN
** C 217 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.097322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.084503 restraints weight = 31666.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.085988 restraints weight = 20466.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.087106 restraints weight = 14829.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.087880 restraints weight = 11657.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.088345 restraints weight = 9800.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6922  Z= 0.217
  Angle     :  0.673   7.684   9456  Z= 0.356
  Chirality :  0.043   0.162   1203
  Planarity :  0.004   0.042   1222
  Dihedral  :  4.596  32.105   1032
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.40 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.91 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.25), residues: 968
  helix: -0.77 (0.24), residues: 448
  sheet: -2.51 (0.86), residues: 41
  loop : -2.23 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 118 
 TYR   0.011   0.001   TYR A  99 
 PHE   0.019   0.002   PHE B 104 
 TRP   0.009   0.001   TRP D 274 
 HIS   0.002   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 6921)
  covalent geometry    : angle       0.67345 ( 9454)
  SS BOND              : bond        0.00510 (    1)
  SS BOND              : angle       0.80910 (    2)
  hydrogen bonds       : bond        0.03770 (  276)
  hydrogen bonds       : angle       4.84855 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   90 PHE cc_start: 0.8567 (m-80) cc_final: 0.8352 (m-80)
REVERT: B   34 PHE cc_start: 0.8245 (p90) cc_final: 0.8009 (p90)
REVERT: B   94 GLN cc_start: 0.9319 (mp-120) cc_final: 0.8993 (mm-40)
REVERT: C   24 MET cc_start: 0.8145 (tmm) cc_final: 0.7858 (tmm)
REVERT: C  180 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8529 (pp30)
  outliers start: 13
  outliers final: 10
  residues processed: 119
  average time/residue: 0.0588
  time to fit residues: 9.9381
Evaluate side-chains
  117 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain C residue    8 ASN
Chi-restraints excluded: chain C residue   20 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  180 GLN
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 71 optimal weight:    0.6980
   chunk 74 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 88 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A   7 HIS
** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.098094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.085565 restraints weight = 31088.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.087035 restraints weight = 20602.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.088082 restraints weight = 15071.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.088738 restraints weight = 12021.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.089236 restraints weight = 10256.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6922  Z= 0.134
  Angle     :  0.596   8.056   9456  Z= 0.309
  Chirality :  0.042   0.138   1203
  Planarity :  0.003   0.034   1222
  Dihedral  :  4.147  22.824   1029
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.68 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.64 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.26), residues: 968
  helix: -0.18 (0.25), residues: 445
  sheet: -2.29 (0.85), residues: 46
  loop : -2.18 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 243 
 TYR   0.007   0.001   TYR D  52 
 PHE   0.012   0.001   PHE D  35 
 TRP   0.009   0.001   TRP D 274 
 HIS   0.002   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6921)
  covalent geometry    : angle       0.59608 ( 9454)
  SS BOND              : bond        0.00347 (    1)
  SS BOND              : angle       0.60975 (    2)
  hydrogen bonds       : bond        0.03313 (  276)
  hydrogen bonds       : angle       4.57141 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  100 ASP cc_start: 0.8595 (m-30) cc_final: 0.8232 (m-30)
REVERT: C   24 MET cc_start: 0.8140 (tmm) cc_final: 0.7885 (tmm)
REVERT: C  225 MET cc_start: 0.8038 (mmp) cc_final: 0.7654 (mmp)
  outliers start: 13
  outliers final: 7
  residues processed: 118
  average time/residue: 0.0633
  time to fit residues: 10.5277
Evaluate side-chains
  108 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain C residue   20 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0980
   chunk 83 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 70 optimal weight:    0.1980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A   7 HIS
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 GLN
** D 101 GLN ** 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 = 0.3853 r_free = 0.3853 target = 0.099266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.087164 restraints weight = 28130.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.088656 restraints weight = 18146.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.089700 restraints weight = 13061.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.090473 restraints weight = 10296.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.091028 restraints weight = 8497.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6922  Z= 0.109
  Angle     :  0.573   8.271   9456  Z= 0.293
  Chirality :  0.041   0.160   1203
  Planarity :  0.003   0.033   1222
  Dihedral  :  3.985  23.856   1029
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.48 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 20.42 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.51 (0.27), residues: 968
  helix:  0.18 (0.25), residues: 449
  sheet: -2.15 (0.88), residues: 44
  loop : -2.10 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  88 
 TYR   0.004   0.001   TYR D 294 
 PHE   0.012   0.001   PHE A  90 
 TRP   0.008   0.001   TRP D 274 
 HIS   0.001   0.000   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6921)
  covalent geometry    : angle       0.57298 ( 9454)
  SS BOND              : bond        0.00250 (    1)
  SS BOND              : angle       0.46288 (    2)
  hydrogen bonds       : bond        0.02863 (  276)
  hydrogen bonds       : angle       4.35556 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.216 
Fit side-chains
REVERT: C   20 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6114 (mmp)
REVERT: C  180 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7904 (pp30)
REVERT: C  225 MET cc_start: 0.8220 (mmp) cc_final: 0.7854 (mmp)
REVERT: C  276 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8542 (mm)
  outliers start: 15
  outliers final: 8
  residues processed: 118
  average time/residue: 0.0596
  time to fit residues: 10.0062
Evaluate side-chains
  117 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain C residue    8 ASN
Chi-restraints excluded: chain C residue   20 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue  180 GLN
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 89 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 93 optimal weight:    0.2980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A   7 HIS
** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 GLN
** D 101 GLN ** 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 = 0.3761 r_free = 0.3761 target = 0.095239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.082316 restraints weight = 31896.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.083954 restraints weight = 19735.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.085101 restraints weight = 13977.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.085842 restraints weight = 10750.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.086440 restraints weight = 8930.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6922  Z= 0.176
  Angle     :  0.622   8.414   9456  Z= 0.323
  Chirality :  0.042   0.157   1203
  Planarity :  0.003   0.032   1222
  Dihedral  :  4.144  25.282   1029
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.82 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.72 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.27), residues: 968
  helix:  0.23 (0.25), residues: 448
  sheet: -2.46 (0.84), residues: 46
  loop : -2.07 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 118 
 TYR   0.006   0.001   TYR A  99 
 PHE   0.013   0.001   PHE A  90 
 TRP   0.007   0.001   TRP C 274 
 HIS   0.002   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 6921)
  covalent geometry    : angle       0.62207 ( 9454)
  SS BOND              : bond        0.00399 (    1)
  SS BOND              : angle       0.86266 (    2)
  hydrogen bonds       : bond        0.03155 (  276)
  hydrogen bonds       : angle       4.42849 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.271 
Fit side-chains
REVERT: B   94 GLN cc_start: 0.9393 (mp-120) cc_final: 0.9083 (mm-40)
REVERT: B  205 MET cc_start: 0.7678 (pmm) cc_final: 0.6972 (pmm)
REVERT: C   20 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6794 (mmp)
REVERT: C  129 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8437 (ptpp)
REVERT: C  180 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8096 (pp30)
REVERT: C  225 MET cc_start: 0.8034 (mmp) cc_final: 0.7706 (mmp)
REVERT: C  276 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: D   24 MET cc_start: 0.7626 (tpt) cc_final: 0.7238 (tpt)
REVERT: D  191 MET cc_start: 0.9128 (tpp) cc_final: 0.8712 (tpt)
  outliers start: 25
  outliers final: 14
  residues processed: 125
  average time/residue: 0.0558
  time to fit residues: 10.0173
Evaluate side-chains
  120 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue    8 ASN
Chi-restraints excluded: chain C residue   20 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  129 LYS
Chi-restraints excluded: chain C residue  176 VAL
Chi-restraints excluded: chain C residue  180 GLN
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  276 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 73 optimal weight:    0.5980
   chunk 88 optimal weight:    0.1980
   chunk 26 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 180 GLN
** D 101 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.096397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.083796 restraints weight = 29185.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.085316 restraints weight = 18094.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.086409 restraints weight = 12953.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.087260 restraints weight = 9878.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.087542 restraints weight = 8181.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6922  Z= 0.122
  Angle     :  0.596   8.682   9456  Z= 0.304
  Chirality :  0.042   0.191   1203
  Planarity :  0.003   0.032   1222
  Dihedral  :  4.046  25.101   1029
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.30 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.34 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.41 (0.27), residues: 968
  helix:  0.34 (0.25), residues: 449
  sheet: -2.86 (0.85), residues: 41
  loop : -2.06 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  88 
 TYR   0.004   0.001   TYR A  99 
 PHE   0.011   0.001   PHE A  90 
 TRP   0.008   0.001   TRP D 274 
 HIS   0.003   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6921)
  covalent geometry    : angle       0.59588 ( 9454)
  SS BOND              : bond        0.00302 (    1)
  SS BOND              : angle       0.65206 (    2)
  hydrogen bonds       : bond        0.02888 (  276)
  hydrogen bonds       : angle       4.27497 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.277 
Fit side-chains
REVERT: B   88 GLN cc_start: 0.8566 (tt0) cc_final: 0.8240 (tt0)
REVERT: B   94 GLN cc_start: 0.9369 (mp-120) cc_final: 0.9087 (mm-40)
REVERT: B  205 MET cc_start: 0.7601 (pmm) cc_final: 0.6916 (pmm)
REVERT: C   20 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6668 (mmp)
REVERT: C  180 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7759 (pp30)
REVERT: C  225 MET cc_start: 0.8124 (mmp) cc_final: 0.7712 (mmp)
REVERT: D   24 MET cc_start: 0.7546 (tpt) cc_final: 0.7177 (tpt)
REVERT: D  191 MET cc_start: 0.9042 (tpp) cc_final: 0.8655 (tpt)
  outliers start: 22
  outliers final: 15
  residues processed: 125
  average time/residue: 0.0694
  time to fit residues: 12.3615
Evaluate side-chains
  124 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain C residue    8 ASN
Chi-restraints excluded: chain C residue   20 MET
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  180 GLN
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0570
   chunk 94 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0470
   chunk 54 optimal weight:    0.0270
   chunk 52 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 44 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0020
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.1462

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

Flipped N/Q/H residues before XYZ refinement:
A  88 GLN
C 180 GLN
** D 101 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.098151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.085435 restraints weight = 29469.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.087056 restraints weight = 18060.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.088222 restraints weight = 12736.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.089076 restraints weight = 9731.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.089602 restraints weight = 7890.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   6922  Z= 0.105
  Angle     :  0.592   8.594   9456  Z= 0.297
  Chirality :  0.041   0.180   1203
  Planarity :  0.003   0.032   1222
  Dihedral  :  3.862  24.437   1029
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.06 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.96 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.21 (0.27), residues: 968
  helix:  0.55 (0.26), residues: 449
  sheet: -2.29 (0.86), residues: 44
  loop : -2.06 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  88 
 TYR   0.005   0.000   TYR C  52 
 PHE   0.009   0.001   PHE B 104 
 TRP   0.007   0.001   TRP D 274 
 HIS   0.002   0.000   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6921)
  covalent geometry    : angle       0.59193 ( 9454)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       0.42903 (    2)
  hydrogen bonds       : bond        0.02617 (  276)
  hydrogen bonds       : angle       4.17172 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8977 (tptp) cc_final: 0.8597 (tptt)
REVERT: B   94 GLN cc_start: 0.9373 (mp-120) cc_final: 0.9095 (mm-40)
REVERT: B  205 MET cc_start: 0.7558 (pmm) cc_final: 0.6944 (pmm)
REVERT: C   24 MET cc_start: 0.8197 (tmm) cc_final: 0.7851 (tmm)
REVERT: C  225 MET cc_start: 0.8152 (mmp) cc_final: 0.7769 (mmp)
REVERT: D   24 MET cc_start: 0.7500 (tpt) cc_final: 0.7123 (tpt)
REVERT: D  191 MET cc_start: 0.9028 (tpp) cc_final: 0.8573 (tpt)
REVERT: D  274 TRP cc_start: 0.7514 (t-100) cc_final: 0.7140 (t-100)
  outliers start: 17
  outliers final: 12
  residues processed: 130
  average time/residue: 0.0680
  time to fit residues: 12.5707
Evaluate side-chains
  125 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 6 optimal weight:    0.0980
   chunk 62 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0270
   chunk 76 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   overall best weight:    0.4016

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
** D 101 GLN ** 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 = 0.3831 r_free = 0.3831 target = 0.098138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.085466 restraints weight = 28926.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.087005 restraints weight = 17950.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.088116 restraints weight = 12727.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.088946 restraints weight = 9809.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.089278 restraints weight = 8021.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6922  Z= 0.110
  Angle     :  0.600   8.916   9456  Z= 0.301
  Chirality :  0.041   0.181   1203
  Planarity :  0.003   0.030   1222
  Dihedral  :  3.784  24.248   1029
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.58 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.31 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.27), residues: 968
  helix:  0.61 (0.26), residues: 449
  sheet: -2.23 (0.87), residues: 44
  loop : -2.04 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  88 
 TYR   0.004   0.001   TYR C 288 
 PHE   0.011   0.001   PHE A  90 
 TRP   0.006   0.001   TRP D 274 
 HIS   0.002   0.000   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6921)
  covalent geometry    : angle       0.60026 ( 9454)
  SS BOND              : bond        0.00189 (    1)
  SS BOND              : angle       0.48166 (    2)
  hydrogen bonds       : bond        0.02602 (  276)
  hydrogen bonds       : angle       4.11216 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 GLU cc_start: 0.8585 (pt0) cc_final: 0.8305 (pt0)
REVERT: B  205 MET cc_start: 0.7559 (pmm) cc_final: 0.6871 (pmm)
REVERT: C  225 MET cc_start: 0.8190 (mmp) cc_final: 0.7791 (mmp)
REVERT: D   24 MET cc_start: 0.7517 (tpt) cc_final: 0.7239 (tpt)
REVERT: D  129 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7654 (pttm)
REVERT: D  191 MET cc_start: 0.9034 (tpp) cc_final: 0.8406 (tpt)
REVERT: D  274 TRP cc_start: 0.7553 (t-100) cc_final: 0.7170 (t-100)
  outliers start: 18
  outliers final: 14
  residues processed: 127
  average time/residue: 0.0676
  time to fit residues: 12.1917
Evaluate side-chains
  126 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain C residue    8 ASN
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0570
   chunk 2 optimal weight:    5.9990
   chunk 65 optimal weight:    0.3980
   chunk 63 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** 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 = 0.3806 r_free = 0.3806 target = 0.096875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.083941 restraints weight = 29199.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.085549 restraints weight = 17886.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.086699 restraints weight = 12559.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.087572 restraints weight = 9644.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.088037 restraints weight = 7877.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6922  Z= 0.123
  Angle     :  0.611   9.008   9456  Z= 0.308
  Chirality :  0.042   0.173   1203
  Planarity :  0.003   0.029   1222
  Dihedral  :  3.788  24.276   1029
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.58 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.31 %
    Favored  : 72.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.27), residues: 968
  helix:  0.63 (0.26), residues: 449
  sheet: -2.26 (0.87), residues: 44
  loop : -2.03 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  88 
 TYR   0.003   0.001   TYR D  52 
 PHE   0.025   0.001   PHE A  90 
 TRP   0.006   0.001   TRP C 274 
 HIS   0.002   0.000   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6921)
  covalent geometry    : angle       0.61104 ( 9454)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.58751 (    2)
  hydrogen bonds       : bond        0.02670 (  276)
  hydrogen bonds       : angle       4.14984 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8284 (tt0)
REVERT: B   94 GLN cc_start: 0.9379 (mp-120) cc_final: 0.9104 (mm-40)
REVERT: B  205 MET cc_start: 0.7594 (pmm) cc_final: 0.6902 (pmm)
REVERT: C  225 MET cc_start: 0.8126 (mmp) cc_final: 0.7740 (mmp)
REVERT: D   24 MET cc_start: 0.7560 (tpt) cc_final: 0.7234 (tpt)
REVERT: D  129 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7661 (pttm)
REVERT: D  191 MET cc_start: 0.9090 (tpp) cc_final: 0.8385 (tpt)
REVERT: D  274 TRP cc_start: 0.7575 (t-100) cc_final: 0.7195 (t-100)
  outliers start: 17
  outliers final: 13
  residues processed: 121
  average time/residue: 0.0653
  time to fit residues: 11.2594
Evaluate side-chains
  122 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain C residue    8 ASN
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    0.0060
   chunk 74 optimal weight:    0.4980
   chunk 76 optimal weight:    4.9990
   chunk 46 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** 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 = 0.3816 r_free = 0.3816 target = 0.097291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.084712 restraints weight = 28659.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.086218 restraints weight = 17660.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.087338 restraints weight = 12571.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.088016 restraints weight = 9726.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.088717 restraints weight = 8096.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6922  Z= 0.118
  Angle     :  0.614   9.199   9456  Z= 0.308
  Chirality :  0.042   0.173   1203
  Planarity :  0.003   0.029   1222
  Dihedral  :  3.815  24.200   1029
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.58 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 24.64 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.27), residues: 968
  helix:  0.64 (0.25), residues: 449
  sheet: -2.28 (0.86), residues: 44
  loop : -2.04 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  88 
 TYR   0.003   0.001   TYR C 255 
 PHE   0.026   0.001   PHE A  90 
 TRP   0.006   0.001   TRP C 274 
 HIS   0.002   0.000   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6921)
  covalent geometry    : angle       0.61433 ( 9454)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.56815 (    2)
  hydrogen bonds       : bond        0.02632 (  276)
  hydrogen bonds       : angle       4.16035 (  807)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8923 (tptp) cc_final: 0.8654 (tptt)
REVERT: B   94 GLN cc_start: 0.9364 (mp-120) cc_final: 0.9099 (mm-40)
REVERT: B  205 MET cc_start: 0.7580 (pmm) cc_final: 0.6916 (pmm)
REVERT: C  225 MET cc_start: 0.8150 (mmp) cc_final: 0.7757 (mmp)
REVERT: D   24 MET cc_start: 0.7573 (tpt) cc_final: 0.7258 (tpt)
REVERT: D  129 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7623 (pttm)
REVERT: D  191 MET cc_start: 0.9060 (tpp) cc_final: 0.8376 (tpt)
REVERT: D  274 TRP cc_start: 0.7573 (t-100) cc_final: 0.7188 (t60)
  outliers start: 18
  outliers final: 15
  residues processed: 124
  average time/residue: 0.0679
  time to fit residues: 12.0372
Evaluate side-chains
  124 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 ILE
Chi-restraints excluded: chain A residue  154 PHE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain B residue   75 HIS
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   88 GLN
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain C residue    8 ASN
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   56 VAL
Chi-restraints excluded: chain D residue  129 LYS
Chi-restraints excluded: chain D residue  209 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    0.0470
   chunk 21 optimal weight:    0.0870
   chunk 85 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0070
   chunk 89 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
B  88 GLN
** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 101 GLN ** 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 = 0.3809 r_free = 0.3809 target = 0.096810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.084516 restraints weight = 28356.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.085988 restraints weight = 17914.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.087067 restraints weight = 12765.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.087785 restraints weight = 9977.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.088416 restraints weight = 8324.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6922  Z= 0.124
  Angle     :  0.630   9.226   9456  Z= 0.314
  Chirality :  0.042   0.170   1203
  Planarity :  0.003   0.029   1222
  Dihedral  :  3.842  24.234   1029
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  5.89 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 24.96 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.27), residues: 968
  helix:  0.56 (0.25), residues: 455
  sheet: -2.29 (0.87), residues: 44
  loop : -2.03 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 118 
 TYR   0.003   0.001   TYR C 255 
 PHE   0.027   0.001   PHE A  90 
 TRP   0.006   0.001   TRP C 274 
 HIS   0.002   0.000   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6921)
  covalent geometry    : angle       0.63043 ( 9454)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       0.62851 (    2)
  hydrogen bonds       : bond        0.02664 (  276)
  hydrogen bonds       : angle       4.16714 (  807)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1243.81 seconds
wall clock time: 22 minutes 7.57 seconds (1327.57 seconds total)