Starting phenix.real_space_refine
on Sat Aug 23 02:17:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i6o_35201/08_2025/8i6o_35201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i6o_35201/08_2025/8i6o_35201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i6o_35201/08_2025/8i6o_35201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i6o_35201/08_2025/8i6o_35201.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i6o_35201/08_2025/8i6o_35201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i6o_35201/08_2025/8i6o_35201.map"
  }
  resolution = 3.8
  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=  -0.001 sd=   0.047
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      20      5.16       5
     C    5876      2.51       5
     N    1498      2.21       5
     O    1690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9084
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2299
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 40
    Chain: "B"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1680
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 2299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2299
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 12, 'TRANS': 288}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 20}
          Unresolved non-hydrogen planarities: 40
    Chain: "D"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1680
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'ARG:plan': 22}
          Unresolved non-hydrogen planarities: 44
    Chain: "E"
      Number of atoms: 1126
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1126
          Classifications: {'peptide': 150}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 1, 'TRANS': 148}
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 124
          Unresolved non-hydrogen dihedrals: 66
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 12, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 64
  Time building chain proxies: 2.48, per 1000 atoms: 0.27
  Number of scatterers: 9084
  At special positions: 0
  Unit cell: (78.455, 81.77, 233.155, 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      20     16.00
     O    1690      8.00
     N    1498      7.00
     C    5876      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 387.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2186

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      61.9% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 54
      removed outlier: 3.735A  pdb=" N   HIS A  41 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 84
      removed outlier: 3.887A  pdb=" N   SER A  59 " --> pdb=" O   HIS A  55 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 4.407A  pdb=" N   TRP A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLN A  91 " --> pdb=" O   GLY A  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 86 through 91'
    Processing helix  chain 'A' and resid 105 through 118
    Processing helix  chain 'A' and resid 129 through 142
    Processing helix  chain 'A' and resid 167 through 179
      removed outlier: 3.673A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 234
      removed outlier: 3.859A  pdb=" N   ARG A 196 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   GLY A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ARG A 234 " --> pdb=" O   HIS A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 244
    Processing helix  chain 'A' and resid 247 through 272
      Proline residue:  A 254  - end of helix
    Processing helix  chain 'A' and resid 273 through 293
      removed outlier: 3.891A  pdb=" N   GLY A 283 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   SER A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   VAL A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL A 286 " --> pdb=" O   ASN A 282 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ASN A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 332
    Processing helix  chain 'B' and resid 41 through 49
      removed outlier: 4.117A  pdb=" N   LEU B  45 " --> pdb=" O   LYS B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.554A  pdb=" N   GLN B  80 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ILE B  81 " --> pdb=" O   ARG B  78 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 77 through 81'
    Processing helix  chain 'B' and resid 95 through 100
    Processing helix  chain 'B' and resid 101 through 108
      removed outlier: 3.931A  pdb=" N   GLN B 105 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE B 106 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 125
      removed outlier: 3.907A  pdb=" N   ILE B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ALA B 115 " --> pdb=" O   LYS B 111 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   LYS B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL B 125 " --> pdb=" O   ALA B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 151
      removed outlier: 4.036A  pdb=" N   ALA B 151 " --> pdb=" O   GLY B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 186
      removed outlier: 3.863A  pdb=" N   SER B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   GLU B 175 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU B 186 " --> pdb=" O   ASP B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'C' and resid 36 through 54
    Processing helix  chain 'C' and resid 60 through 75
      removed outlier: 3.748A  pdb=" N   GLY C  67 " --> pdb=" O   CYS C  63 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU C  70 " --> pdb=" O   MET C  66 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU C  72 " --> pdb=" O   ILE C  68 " (cutoff:3.500A)
      Proline residue:  C  73  - end of helix
    Processing helix  chain 'C' and resid 76 through 86
    Processing helix  chain 'C' and resid 105 through 119
    Processing helix  chain 'C' and resid 129 through 140
      removed outlier: 3.989A  pdb=" N   GLN C 140 " --> pdb=" O   GLU C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 180
      removed outlier: 4.019A  pdb=" N   GLU C 180 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 195
    Processing helix  chain 'C' and resid 197 through 233
      removed outlier: 3.547A  pdb=" N   LEU C 201 " --> pdb=" O   LEU C 197 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS C 202 " --> pdb=" O   SER C 198 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ILE C 227 " --> pdb=" O   VAL C 223 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ASN C 233 " --> pdb=" O   LEU C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 244
    Processing helix  chain 'C' and resid 247 through 292
      removed outlier: 3.786A  pdb=" N   VAL C 251 " --> pdb=" O   THR C 247 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ARG C 252 " --> pdb=" O   ASP C 248 " (cutoff:3.500A)
      Proline residue:  C 254  - end of helix
      removed outlier: 3.655A  pdb=" N   ASN C 279 " --> pdb=" O   ALA C 275 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY C 283 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   SER C 284 " --> pdb=" O   TRP C 280 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   VAL C 285 " --> pdb=" O   LEU C 281 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL C 286 " --> pdb=" O   ASN C 282 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   ASN C 287 " --> pdb=" O   GLY C 283 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR C 292 " --> pdb=" O   LEU C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 302 through 313
    Processing helix  chain 'C' and resid 319 through 332
      removed outlier: 3.938A  pdb=" N   ALA C 326 " --> pdb=" O   TRP C 322 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG C 327 " --> pdb=" O   LEU C 323 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   HIS C 328 " --> pdb=" O   ALA C 324 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG C 330 " --> pdb=" O   ALA C 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 39
    Processing helix  chain 'D' and resid 40 through 49
      removed outlier: 3.696A  pdb=" N   ILE D  48 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LEU D  49 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 79
      removed outlier: 3.576A  pdb=" N   ARG D  79 " --> pdb=" O   PRO D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 100
    Processing helix  chain 'D' and resid 101 through 108
    Processing helix  chain 'D' and resid 110 through 126
      removed outlier: 3.710A  pdb=" N   GLU D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ARG D 124 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 151
      removed outlier: 3.909A  pdb=" N   ALA D 151 " --> pdb=" O   GLY D 147 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 186
      removed outlier: 4.077A  pdb=" N   GLU D 175 " --> pdb=" O   ARG D 171 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ILE D 176 " --> pdb=" O   LEU D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 201
      removed outlier: 3.650A  pdb=" N   ALA D 201 " --> pdb=" O   ALA D 198 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 98
      removed outlier: 3.777A  pdb=" N   LEU E  57 " --> pdb=" O   VAL E  53 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLN E  70 " --> pdb=" O   ASP E  66 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 99 through 116
      removed outlier: 3.765A  pdb=" N   GLN E 103 " --> pdb=" O   ARG E  99 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 126
      removed outlier: 3.844A  pdb=" N   LEU E 126 " --> pdb=" O   LEU E 122 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 135 through 186
      removed outlier: 3.992A  pdb=" N   ILE E 169 " --> pdb=" O   VAL E 165 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 187 through 200
      removed outlier: 4.068A  pdb=" N   ALA E 191 " --> pdb=" O   ARG E 187 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLN E 198 " --> pdb=" O   ARG E 194 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   GLN E 199 " --> pdb=" O   LYS E 195 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ALA E 200 " --> pdb=" O   GLU E 196 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97
      removed outlier: 6.844A  pdb=" N   VAL A 158 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   LEU A 127 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   SER A 160 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   ALA A 125 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   THR A 162 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 21
      removed outlier: 5.443A  pdb=" N   VAL B   7 " --> pdb=" O   GLU B  20 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   PHE B   4 " --> pdb=" O   LEU B  60 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   LEU B  60 " --> pdb=" O   PHE B   4 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   GLN B   6 " --> pdb=" O   LYS B  58 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   LYS B  58 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 83
      removed outlier: 7.007A  pdb=" N   GLY B  82 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 211
      removed outlier: 7.307A  pdb=" N   THR B 209 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 125 through 128
      removed outlier: 3.504A  pdb=" N   GLN C 126 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   VAL C 158 " --> pdb=" O   ILE C 128 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLN C 186 " --> pdb=" O   PHE C  99 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 8
      removed outlier: 3.927A  pdb=" N   GLU D   5 " --> pdb=" O   LYS D  58 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS D  58 " --> pdb=" O   GLU D   5 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   VAL D   7 " --> pdb=" O   SER D  56 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   SER D  56 " --> pdb=" O   VAL D   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 33
      removed outlier: 6.652A  pdb=" N   PHE D  32 " --> pdb=" O   LEU D 208 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG D 219 " --> pdb=" O   MET D 207 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 81 through 84
      removed outlier: 3.657A  pdb=" N   ASP D 162 " --> pdb=" O   VAL D  84 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ALA D 161 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1512 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.39 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: 2982
        1.34 -     1.46: 1047
        1.46 -     1.58: 5159
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 9226
  Sorted by residual:
  bond pdb=" C   ILE E 144 "
       pdb=" O   ILE E 144 "
    ideal  model  delta    sigma   weight residual
    1.237  1.220  0.017 1.29e-02 6.01e+03 1.82e+00
  bond pdb=" CA  GLU D 163 "
       pdb=" CB  GLU D 163 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.33e+00
  bond pdb=" CG  GLU C 114 "
       pdb=" CD  GLU C 114 "
    ideal  model  delta    sigma   weight residual
    1.516  1.488  0.028 2.50e-02 1.60e+03 1.27e+00
  bond pdb=" CD  GLU C 114 "
       pdb=" OE1 GLU C 114 "
    ideal  model  delta    sigma   weight residual
    1.249  1.228  0.021 1.90e-02 2.77e+03 1.18e+00
  bond pdb=" N   LYS D 130 "
       pdb=" CA  LYS D 130 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.40e-01
  ... (remaining 9221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 12157
        1.86 -     3.72: 239
        3.72 -     5.57: 45
        5.57 -     7.43: 8
        7.43 -     9.29: 3
  Bond angle restraints: 12452
  Sorted by residual:
  angle pdb=" N   VAL C 319 "
        pdb=" CA  VAL C 319 "
        pdb=" C   VAL C 319 "
      ideal   model   delta    sigma   weight residual
     111.62  108.52    3.10 7.90e-01 1.60e+00 1.54e+01
  angle pdb=" N   GLU C 114 "
        pdb=" CA  GLU C 114 "
        pdb=" CB  GLU C 114 "
      ideal   model   delta    sigma   weight residual
     110.28  116.11   -5.83 1.55e+00 4.16e-01 1.41e+01
  angle pdb=" C   ARG C 113 "
        pdb=" N   GLU C 114 "
        pdb=" CA  GLU C 114 "
      ideal   model   delta    sigma   weight residual
     120.31  115.50    4.81 1.52e+00 4.33e-01 1.00e+01
  angle pdb=" CB  LYS E 173 "
        pdb=" CG  LYS E 173 "
        pdb=" CD  LYS E 173 "
      ideal   model   delta    sigma   weight residual
     111.30  118.02   -6.72 2.30e+00 1.89e-01 8.53e+00
  angle pdb=" N   GLY C  58 "
        pdb=" CA  GLY C  58 "
        pdb=" C   GLY C  58 "
      ideal   model   delta    sigma   weight residual
     111.10  107.05    4.05 1.46e+00 4.69e-01 7.70e+00
  ... (remaining 12447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 4961
       17.96 -    35.92: 561
       35.92 -    53.88: 87
       53.88 -    71.84: 21
       71.84 -    89.81: 8
  Dihedral angle restraints: 5638
    sinusoidal: 2242
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" CA  LEU C 316 "
           pdb=" C   LEU C 316 "
           pdb=" N   GLY C 317 "
           pdb=" CA  GLY C 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.65   20.35     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" CA  PRO E 131 "
           pdb=" C   PRO E 131 "
           pdb=" N   GLU E 132 "
           pdb=" CA  GLU E 132 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.09   19.91     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  HIS B  19 "
           pdb=" C   HIS B  19 "
           pdb=" N   GLU B  20 "
           pdb=" CA  GLU B  20 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.70   17.30     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 5635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 951
       0.032 -    0.063: 347
       0.063 -    0.095: 126
       0.095 -    0.127: 53
       0.127 -    0.158: 5
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" CB  ILE E 169 "
            pdb=" CA  ILE E 169 "
            pdb=" CG1 ILE E 169 "
            pdb=" CG2 ILE E 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.27e-01
  chirality pdb=" CG  LEU E 183 "
            pdb=" CB  LEU E 183 "
            pdb=" CD1 LEU E 183 "
            pdb=" CD2 LEU E 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  GLN E 172 "
            pdb=" N   GLN E 172 "
            pdb=" C   GLN E 172 "
            pdb=" CB  GLN E 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.11e-01
  ... (remaining 1479 not shown)

  Planarity restraints: 1559
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 153 "    0.036 5.00e-02 4.00e+02   5.41e-02 4.68e+00
        pdb=" N   PRO A 154 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 154 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 154 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 109 "    0.030 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO B 110 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B 110 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 110 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 134 "   -0.029 5.00e-02 4.00e+02   4.48e-02 3.21e+00
        pdb=" N   PRO B 135 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 135 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 135 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1556 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 133
        2.69 -     3.24: 9205
        3.24 -     3.79: 13611
        3.79 -     4.35: 16723
        4.35 -     4.90: 26606
  Nonbonded interactions: 66278
  Sorted by model distance:
  nonbonded pdb=" O   GLN E 151 "
            pdb=" OG  SER E 154 "
     model   vdw
     2.135 3.040
  nonbonded pdb=" OG  SER C 105 "
            pdb=" OD1 ASN C 107 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" OE1 GLN B   6 "
            pdb=" OG  SER B  22 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   ARG D  27 "
            pdb=" OG1 THR D 189 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD1 ASP A 101 "
            pdb=" OG1 THR A 104 "
     model   vdw
     2.262 3.040
  ... (remaining 66273 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             5.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.960
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
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      :  0.003   0.035   9226  Z= 0.139
  Angle     :  0.664   9.289  12452  Z= 0.348
  Chirality :  0.041   0.158   1482
  Planarity :  0.004   0.054   1559
  Dihedral  : 15.305  89.805   3452
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  1.84 %
    Favored  : 97.54 %
  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:  0.14 (0.25), residues: 1186
  helix:  1.61 (0.21), residues: 696
  sheet: -1.53 (0.67), residues: 66
  loop : -2.34 (0.26), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 104 
 TYR   0.014   0.001   TYR E 114 
 PHE   0.020   0.001   PHE E 155 
 TRP   0.013   0.001   TRP A  90 
 HIS   0.007   0.001   HIS E 130 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9226)
  covalent geometry    : angle       0.66418 (12452)
  hydrogen bonds       : bond        0.17643 (  512)
  hydrogen bonds       : angle       5.80571 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.8636 (m-30) cc_final: 0.8331 (m-30)
REVERT: B  163 GLU cc_start: 0.8195 (tp30) cc_final: 0.7943 (tp30)
REVERT: B  196 ASP cc_start: 0.8807 (t0) cc_final: 0.8124 (p0)
REVERT: B  207 MET cc_start: 0.8162 (ptp) cc_final: 0.7544 (ptm)
REVERT: B  209 THR cc_start: 0.8036 (m) cc_final: 0.7626 (t)
REVERT: C  124 GLU cc_start: 0.8257 (pp20) cc_final: 0.8010 (pp20)
REVERT: D  116 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8755 (pttm)
REVERT: D  169 ASP cc_start: 0.8462 (t0) cc_final: 0.8213 (t0)
REVERT: E  169 ILE cc_start: 0.8959 (tp) cc_final: 0.8754 (tp)
  outliers start: 6
  outliers final: 6
  residues processed: 171
  average time/residue: 0.0936
  time to fit residues: 22.8493
Evaluate side-chains
  133 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  148 ARG
Chi-restraints excluded: chain E residue  186 ARG
Chi-restraints excluded: chain E residue  194 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0370
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0050
   overall best weight:    0.4472

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

Flipped N/Q/H residues before XYZ refinement:
** B  87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  95 GLN
D  19 HIS
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.146668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.107042 restraints weight = 21455.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.109951 restraints weight = 11671.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.110398 restraints weight = 7856.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.111130 restraints weight = 6537.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.111299 restraints weight = 6349.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9226  Z= 0.141
  Angle     :  0.633   7.496  12452  Z= 0.322
  Chirality :  0.040   0.132   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  6.145  58.243   1234
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.01 %
    Favored  : 85.35 %
  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:  0.32 (0.25), residues: 1186
  helix:  1.83 (0.21), residues: 704
  sheet: -1.48 (0.67), residues: 64
  loop : -2.48 (0.26), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 148 
 TYR   0.011   0.001   TYR E 140 
 PHE   0.014   0.001   PHE E 155 
 TRP   0.014   0.001   TRP A 318 
 HIS   0.008   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9226)
  covalent geometry    : angle       0.63310 (12452)
  hydrogen bonds       : bond        0.05843 (  512)
  hydrogen bonds       : angle       4.75225 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  164 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7993 (mmtp)
REVERT: B  129 GLU cc_start: 0.7882 (pt0) cc_final: 0.7661 (pp20)
REVERT: B  207 MET cc_start: 0.8075 (ptp) cc_final: 0.7153 (ptm)
REVERT: B  209 THR cc_start: 0.8050 (m) cc_final: 0.7622 (t)
REVERT: C  103 LYS cc_start: 0.8075 (tppt) cc_final: 0.7709 (pttt)
REVERT: C  167 ASP cc_start: 0.7880 (p0) cc_final: 0.7585 (m-30)
REVERT: D  116 LYS cc_start: 0.8948 (ptpp) cc_final: 0.8641 (pttm)
REVERT: D  169 ASP cc_start: 0.7901 (t0) cc_final: 0.7407 (t0)
REVERT: E  143 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6648 (t80)
REVERT: E  169 ILE cc_start: 0.8935 (tp) cc_final: 0.8602 (tp)
REVERT: E  173 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7673 (mmtt)
  outliers start: 16
  outliers final: 13
  residues processed: 149
  average time/residue: 0.0889
  time to fit residues: 19.0980
Evaluate side-chains
  145 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  186 ARG
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 48 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0770
   chunk 37 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.130587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.088202 restraints weight = 19877.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.090828 restraints weight = 10671.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.092527 restraints weight = 7257.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.093558 restraints weight = 5752.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.094295 restraints weight = 5033.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9226  Z= 0.131
  Angle     :  0.601   8.472  12452  Z= 0.303
  Chirality :  0.039   0.136   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  5.608  55.917   1226
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.32 %
    Favored  : 80.12 %
  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:  0.47 (0.26), residues: 1186
  helix:  1.94 (0.21), residues: 711
  sheet: -1.86 (0.67), residues: 57
  loop : -2.39 (0.26), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E  99 
 TYR   0.013   0.001   TYR E 114 
 PHE   0.013   0.001   PHE E 155 
 TRP   0.012   0.001   TRP A 318 
 HIS   0.006   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9226)
  covalent geometry    : angle       0.60084 (12452)
  hydrogen bonds       : bond        0.05318 (  512)
  hydrogen bonds       : angle       4.45930 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7886 (mmtp)
REVERT: B  129 GLU cc_start: 0.7945 (pt0) cc_final: 0.7657 (pp20)
REVERT: B  207 MET cc_start: 0.8266 (ptp) cc_final: 0.7660 (ptm)
REVERT: B  209 THR cc_start: 0.8150 (m) cc_final: 0.7739 (t)
REVERT: C  114 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8751 (mp0)
REVERT: D  169 ASP cc_start: 0.8000 (t0) cc_final: 0.7492 (t0)
REVERT: E   97 ASP cc_start: 0.9177 (m-30) cc_final: 0.8847 (m-30)
REVERT: E  143 TYR cc_start: 0.7008 (OUTLIER) cc_final: 0.6742 (t80)
  outliers start: 25
  outliers final: 19
  residues processed: 150
  average time/residue: 0.0852
  time to fit residues: 18.4725
Evaluate side-chains
  147 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 78 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0980
   chunk 69 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 81 optimal weight:    0.1980
   chunk 51 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  99 ASN
D 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.130461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.088154 restraints weight = 20063.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.090728 restraints weight = 10826.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.092335 restraints weight = 7365.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 73)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.093520 restraints weight = 5855.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.094044 restraints weight = 5099.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9226  Z= 0.129
  Angle     :  0.606   9.086  12452  Z= 0.298
  Chirality :  0.038   0.143   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  5.323  56.221   1222
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.47 %
    Favored  : 76.74 %
  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:  0.57 (0.26), residues: 1186
  helix:  2.03 (0.21), residues: 711
  sheet: -1.75 (0.67), residues: 57
  loop : -2.37 (0.26), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 148 
 TYR   0.011   0.001   TYR E 114 
 PHE   0.008   0.001   PHE E 155 
 TRP   0.011   0.001   TRP A 318 
 HIS   0.004   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9226)
  covalent geometry    : angle       0.60567 (12452)
  hydrogen bonds       : bond        0.05126 (  512)
  hydrogen bonds       : angle       4.31395 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8374 (t0) cc_final: 0.8109 (t0)
REVERT: A  164 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7830 (mmtp)
REVERT: B  129 GLU cc_start: 0.7904 (pt0) cc_final: 0.7635 (pp20)
REVERT: B  207 MET cc_start: 0.8257 (ptp) cc_final: 0.7631 (ptm)
REVERT: B  209 THR cc_start: 0.8106 (m) cc_final: 0.7700 (t)
REVERT: C  114 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8742 (mp0)
REVERT: C  258 MET cc_start: 0.7530 (ttm) cc_final: 0.7223 (ttm)
REVERT: D  169 ASP cc_start: 0.8075 (t0) cc_final: 0.7565 (t0)
REVERT: E   97 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8756 (m-30)
REVERT: E  143 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6698 (t80)
  outliers start: 37
  outliers final: 19
  residues processed: 161
  average time/residue: 0.0826
  time to fit residues: 19.4352
Evaluate side-chains
  149 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 116 optimal weight:   10.0000
   chunk 68 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 117 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.128722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.086186 restraints weight = 20303.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.088734 restraints weight = 10942.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.090315 restraints weight = 7471.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.091217 restraints weight = 5941.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.091859 restraints weight = 5234.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9226  Z= 0.147
  Angle     :  0.626   9.586  12452  Z= 0.314
  Chirality :  0.039   0.187   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  5.059  55.680   1218
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.52 %
    Favored  : 74.39 %
  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:  0.51 (0.26), residues: 1186
  helix:  1.91 (0.21), residues: 716
  sheet: -1.68 (0.68), residues: 52
  loop : -2.32 (0.26), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E  99 
 TYR   0.011   0.001   TYR E 114 
 PHE   0.010   0.001   PHE C 209 
 TRP   0.011   0.001   TRP A 318 
 HIS   0.005   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9226)
  covalent geometry    : angle       0.62627 (12452)
  hydrogen bonds       : bond        0.05402 (  512)
  hydrogen bonds       : angle       4.34848 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8451 (t0) cc_final: 0.8114 (t0)
REVERT: A  164 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7708 (mmtp)
REVERT: B  129 GLU cc_start: 0.7986 (pt0) cc_final: 0.7743 (pp20)
REVERT: B  143 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7754 (pt0)
REVERT: B  207 MET cc_start: 0.8300 (ptp) cc_final: 0.7640 (ptm)
REVERT: B  209 THR cc_start: 0.8087 (m) cc_final: 0.7683 (t)
REVERT: C  114 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (mp0)
REVERT: C  258 MET cc_start: 0.7579 (ttm) cc_final: 0.7274 (ttm)
REVERT: D  169 ASP cc_start: 0.8161 (t0) cc_final: 0.7737 (t0)
REVERT: E   97 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8652 (m-30)
REVERT: E  143 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6766 (t80)
REVERT: E  150 GLU cc_start: 0.8084 (tp30) cc_final: 0.7817 (tp30)
  outliers start: 40
  outliers final: 29
  residues processed: 155
  average time/residue: 0.0891
  time to fit residues: 19.7453
Evaluate side-chains
  158 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  143 GLN
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain C residue   41 HIS
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  150 ARG
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 55 optimal weight:    0.3980
   chunk 43 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B  88 HIS
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.135840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.100509 restraints weight = 21274.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.101403 restraints weight = 14134.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.101677 restraints weight = 9403.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.102163 restraints weight = 8634.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.102352 restraints weight = 7988.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9226  Z= 0.175
  Angle     :  0.653  11.010  12452  Z= 0.326
  Chirality :  0.040   0.185   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  5.021  47.880   1218
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 21.82 %
    Favored  : 73.77 %
  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:  0.41 (0.25), residues: 1186
  helix:  1.82 (0.20), residues: 718
  sheet: -1.80 (0.67), residues: 52
  loop : -2.36 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E  99 
 TYR   0.013   0.002   TYR B  11 
 PHE   0.014   0.001   PHE E 155 
 TRP   0.012   0.002   TRP A 318 
 HIS   0.005   0.001   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 9226)
  covalent geometry    : angle       0.65256 (12452)
  hydrogen bonds       : bond        0.05895 (  512)
  hydrogen bonds       : angle       4.42363 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 129
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8428 (t0) cc_final: 0.8141 (t0)
REVERT: A  164 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7719 (mmtp)
REVERT: B  191 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8494 (tt)
REVERT: B  207 MET cc_start: 0.8379 (ptp) cc_final: 0.7760 (ptm)
REVERT: B  209 THR cc_start: 0.7997 (m) cc_final: 0.7551 (t)
REVERT: C  114 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8641 (mp0)
REVERT: D  169 ASP cc_start: 0.8228 (t0) cc_final: 0.7822 (t0)
REVERT: E   93 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8617 (mmmt)
REVERT: E   97 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8567 (m-30)
REVERT: E  143 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6725 (t80)
REVERT: E  150 GLU cc_start: 0.7827 (tp30) cc_final: 0.7539 (tp30)
REVERT: E  168 ASP cc_start: 0.7630 (p0) cc_final: 0.7428 (p0)
  outliers start: 43
  outliers final: 31
  residues processed: 161
  average time/residue: 0.0889
  time to fit residues: 20.7635
Evaluate side-chains
  158 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  148 ILE
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  118 ARG
Chi-restraints excluded: chain E residue  130 HIS
Chi-restraints excluded: chain E residue  143 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 115 optimal weight:    0.7980
   chunk 77 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 117 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0770
   chunk 33 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0010
   overall best weight:    0.3544

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

Flipped N/Q/H residues before XYZ refinement:
B 143 GLN
C 230 HIS
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.131624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.089324 restraints weight = 19862.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.091931 restraints weight = 10698.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.093574 restraints weight = 7312.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.094577 restraints weight = 5815.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.095077 restraints weight = 5093.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9226  Z= 0.125
  Angle     :  0.618  10.743  12452  Z= 0.307
  Chirality :  0.039   0.201   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  4.611  45.147   1214
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 23.05 %
    Favored  : 72.75 %
  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:  0.59 (0.26), residues: 1186
  helix:  1.97 (0.21), residues: 718
  sheet: -1.59 (0.69), residues: 52
  loop : -2.31 (0.27), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 186 
 TYR   0.009   0.001   TYR E 114 
 PHE   0.021   0.001   PHE E 155 
 TRP   0.009   0.001   TRP A  90 
 HIS   0.004   0.001   HIS D  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9226)
  covalent geometry    : angle       0.61778 (12452)
  hydrogen bonds       : bond        0.04946 (  512)
  hydrogen bonds       : angle       4.17218 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 129
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  144 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8141 (pp30)
REVERT: B  207 MET cc_start: 0.8227 (ptp) cc_final: 0.7290 (ptm)
REVERT: B  209 THR cc_start: 0.8177 (m) cc_final: 0.7751 (t)
REVERT: C  114 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8764 (mp0)
REVERT: C  167 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7661 (p0)
REVERT: C  258 MET cc_start: 0.7311 (ttm) cc_final: 0.7032 (ttm)
REVERT: D  109 MET cc_start: 0.8145 (mtp) cc_final: 0.7931 (mtm)
REVERT: D  169 ASP cc_start: 0.8163 (t0) cc_final: 0.7748 (t0)
REVERT: E   93 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8810 (mmmt)
REVERT: E   97 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8595 (m-30)
REVERT: E  143 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6746 (t80)
REVERT: E  150 GLU cc_start: 0.8032 (tp30) cc_final: 0.7767 (tp30)
  outliers start: 41
  outliers final: 27
  residues processed: 157
  average time/residue: 0.0893
  time to fit residues: 20.3742
Evaluate side-chains
  154 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain D residue   21 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  126 ASN
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  130 HIS
Chi-restraints excluded: chain E residue  141 TYR
Chi-restraints excluded: chain E residue  143 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 103 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0570
   chunk 50 optimal weight:    2.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    1.1902

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 126 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.132053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.094774 restraints weight = 20771.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.095423 restraints weight = 11704.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.095841 restraints weight = 7997.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.096207 restraints weight = 8377.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.096199 restraints weight = 7096.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   9226  Z= 0.200
  Angle     :  0.711  11.950  12452  Z= 0.351
  Chirality :  0.041   0.183   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  4.756  41.614   1214
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.98 %
    Favored  : 72.13 %
  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:  0.36 (0.25), residues: 1186
  helix:  1.78 (0.20), residues: 721
  sheet: -2.00 (0.63), residues: 57
  loop : -2.39 (0.27), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 148 
 TYR   0.018   0.002   TYR E 140 
 PHE   0.022   0.001   PHE E 155 
 TRP   0.012   0.002   TRP A 318 
 HIS   0.019   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9226)
  covalent geometry    : angle       0.71097 (12452)
  hydrogen bonds       : bond        0.06012 (  512)
  hydrogen bonds       : angle       4.43265 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 126
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 ASP cc_start: 0.8181 (t0) cc_final: 0.7752 (t0)
REVERT: B  144 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8151 (pp30)
REVERT: B  207 MET cc_start: 0.8184 (ptp) cc_final: 0.7511 (ptm)
REVERT: B  209 THR cc_start: 0.8050 (m) cc_final: 0.7636 (t)
REVERT: C  114 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8792 (mp0)
REVERT: C  167 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.7618 (p0)
REVERT: D    9 LYS cc_start: 0.7789 (tttt) cc_final: 0.7454 (ttpt)
REVERT: D  169 ASP cc_start: 0.8196 (t0) cc_final: 0.7763 (t0)
REVERT: E   93 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8777 (mmmt)
REVERT: E   97 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8654 (m-30)
REVERT: E  140 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6918 (t80)
REVERT: E  143 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.6735 (t80)
REVERT: E  150 GLU cc_start: 0.8000 (tp30) cc_final: 0.7728 (tp30)
  outliers start: 38
  outliers final: 29
  residues processed: 152
  average time/residue: 0.0821
  time to fit residues: 17.9353
Evaluate side-chains
  154 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain C residue  310 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  126 ASN
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  118 ARG
Chi-restraints excluded: chain E residue  130 HIS
Chi-restraints excluded: chain E residue  140 TYR
Chi-restraints excluded: chain E residue  143 TYR
Chi-restraints excluded: chain E residue  197 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0970
   chunk 92 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 118 optimal weight:    0.0370
   chunk 65 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0370
   overall best weight:    0.2734

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

Flipped N/Q/H residues before XYZ refinement:
C 230 HIS
D  99 ASN
D 126 ASN
E 180 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.135949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.100810 restraints weight = 20568.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.100832 restraints weight = 11945.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.101134 restraints weight = 9627.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.101553 restraints weight = 7956.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.101853 restraints weight = 7456.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9226  Z= 0.132
  Angle     :  0.669  13.100  12452  Z= 0.330
  Chirality :  0.040   0.214   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  4.675  39.178   1214
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.10 %
    Favored  : 71.21 %
  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:  0.53 (0.26), residues: 1186
  helix:  1.92 (0.21), residues: 719
  sheet: -1.65 (0.68), residues: 52
  loop : -2.36 (0.27), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 148 
 TYR   0.017   0.001   TYR E 140 
 PHE   0.023   0.001   PHE E 155 
 TRP   0.011   0.001   TRP A  90 
 HIS   0.004   0.001   HIS C  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9226)
  covalent geometry    : angle       0.66902 (12452)
  hydrogen bonds       : bond        0.04991 (  512)
  hydrogen bonds       : angle       4.20149 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 LEU cc_start: 0.7920 (mp) cc_final: 0.7126 (mp)
REVERT: A  164 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8105 (mmmm)
REVERT: B  144 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8072 (pp30)
REVERT: B  196 ASP cc_start: 0.8713 (t0) cc_final: 0.7997 (p0)
REVERT: B  207 MET cc_start: 0.8204 (ptp) cc_final: 0.7305 (ptm)
REVERT: B  209 THR cc_start: 0.8064 (m) cc_final: 0.7599 (t)
REVERT: C  114 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8779 (mp0)
REVERT: C  167 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7585 (p0)
REVERT: C  258 MET cc_start: 0.7147 (ttm) cc_final: 0.6855 (ttm)
REVERT: D  109 MET cc_start: 0.8028 (mtp) cc_final: 0.7784 (mtm)
REVERT: D  169 ASP cc_start: 0.8155 (t0) cc_final: 0.7729 (t0)
REVERT: E   93 LYS cc_start: 0.9252 (mmmt) cc_final: 0.8722 (mmmt)
REVERT: E   97 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8654 (m-30)
REVERT: E  140 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6631 (t80)
REVERT: E  143 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6792 (t80)
REVERT: E  150 GLU cc_start: 0.7935 (tp30) cc_final: 0.7639 (tp30)
  outliers start: 36
  outliers final: 25
  residues processed: 153
  average time/residue: 0.0842
  time to fit residues: 18.7494
Evaluate side-chains
  156 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  118 ARG
Chi-restraints excluded: chain E residue  130 HIS
Chi-restraints excluded: chain E residue  140 TYR
Chi-restraints excluded: chain E residue  143 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 117 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 66 optimal weight:    0.2980
   chunk 58 optimal weight:    0.4980
   chunk 113 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0970
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
B 195 HIS
C 230 HIS
D 126 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.136248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.101316 restraints weight = 20655.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.100825 restraints weight = 11860.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.101020 restraints weight = 10289.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.101564 restraints weight = 8325.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.101837 restraints weight = 7739.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9226  Z= 0.131
  Angle     :  0.664  10.774  12452  Z= 0.329
  Chirality :  0.040   0.213   1482
  Planarity :  0.004   0.046   1559
  Dihedral  :  4.590  37.372   1214
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 24.90 %
    Favored  : 71.62 %
  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:  0.57 (0.26), residues: 1186
  helix:  1.96 (0.21), residues: 719
  sheet: -1.63 (0.68), residues: 52
  loop : -2.35 (0.27), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E 104 
 TYR   0.015   0.001   TYR E 140 
 PHE   0.025   0.001   PHE E 155 
 TRP   0.012   0.001   TRP A  90 
 HIS   0.006   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9226)
  covalent geometry    : angle       0.66435 (12452)
  hydrogen bonds       : bond        0.04833 (  512)
  hydrogen bonds       : angle       4.15324 ( 1512)

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

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

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2372 Ramachandran restraints generated.
    1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 LEU cc_start: 0.7862 (mp) cc_final: 0.7045 (mp)
REVERT: B  144 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8352 (tm-30)
REVERT: B  196 ASP cc_start: 0.8642 (t0) cc_final: 0.7909 (p0)
REVERT: B  207 MET cc_start: 0.8195 (ptp) cc_final: 0.7570 (ptm)
REVERT: B  209 THR cc_start: 0.7975 (m) cc_final: 0.7495 (t)
REVERT: C  114 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8779 (mp0)
REVERT: C  119 LEU cc_start: 0.8746 (tp) cc_final: 0.8447 (tt)
REVERT: C  167 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7651 (p0)
REVERT: C  258 MET cc_start: 0.7210 (ttm) cc_final: 0.6947 (ttm)
REVERT: C  315 LEU cc_start: 0.8483 (tp) cc_final: 0.8207 (tp)
REVERT: D  169 ASP cc_start: 0.8158 (t0) cc_final: 0.7726 (t0)
REVERT: E   93 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8703 (mmmt)
REVERT: E   97 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8668 (m-30)
REVERT: E  140 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6610 (t80)
REVERT: E  143 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6823 (t80)
REVERT: E  150 GLU cc_start: 0.7875 (tp30) cc_final: 0.7583 (tp30)
  outliers start: 34
  outliers final: 27
  residues processed: 148
  average time/residue: 0.0845
  time to fit residues: 18.1330
Evaluate side-chains
  158 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   19 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  144 GLN
Chi-restraints excluded: chain B residue  192 ILE
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain C residue   41 HIS
Chi-restraints excluded: chain C residue   49 LEU
Chi-restraints excluded: chain C residue  104 THR
Chi-restraints excluded: chain C residue  114 GLU
Chi-restraints excluded: chain C residue  162 THR
Chi-restraints excluded: chain C residue  167 ASP
Chi-restraints excluded: chain C residue  230 HIS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 LEU
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   98 ASP
Chi-restraints excluded: chain D residue  126 ASN
Chi-restraints excluded: chain D residue  146 VAL
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain E residue   75 GLN
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue   97 ASP
Chi-restraints excluded: chain E residue  118 ARG
Chi-restraints excluded: chain E residue  140 TYR
Chi-restraints excluded: chain E residue  143 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0980
   chunk 118 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 230 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.135274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.100452 restraints weight = 20500.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.099085 restraints weight = 12748.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.099825 restraints weight = 9146.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.100191 restraints weight = 8195.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.100273 restraints weight = 7548.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9226  Z= 0.144
  Angle     :  0.669   9.982  12452  Z= 0.331
  Chirality :  0.040   0.202   1482
  Planarity :  0.004   0.045   1559
  Dihedral  :  4.614  35.947   1214
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 25.31 %
    Favored  : 71.31 %
  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:  0.51 (0.26), residues: 1186
  helix:  1.91 (0.21), residues: 719
  sheet: -1.67 (0.68), residues: 52
  loop : -2.37 (0.27), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E  87 
 TYR   0.015   0.001   TYR E 140 
 PHE   0.025   0.001   PHE E 155 
 TRP   0.012   0.001   TRP A  90 
 HIS   0.006   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9226)
  covalent geometry    : angle       0.66947 (12452)
  hydrogen bonds       : bond        0.05005 (  512)
  hydrogen bonds       : angle       4.19157 ( 1512)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1853.83 seconds
wall clock time: 32 minutes 37.72 seconds (1957.72 seconds total)