Starting phenix.real_space_refine
on Wed Sep 17 12:29:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h78_51913/09_2025/9h78_51913_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h78_51913/09_2025/9h78_51913.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h78_51913/09_2025/9h78_51913.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h78_51913/09_2025/9h78_51913.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h78_51913/09_2025/9h78_51913_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h78_51913/09_2025/9h78_51913_neut.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 508 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      48      5.16       5
     C    5244      2.51       5
     N    1393      2.21       5
     O    1583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8272
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1936
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1936
          Classifications: {'peptide': 244}
          Link IDs: {'PTRANS': 8, 'TRANS': 235}
    Chain: "B"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2235
          Classifications: {'peptide': 289}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 282}
    Chain: "C"
      Number of atoms: 1858
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 1858
          Classifications: {'peptide': 234}
          Link IDs: {'PTRANS': 7, 'TRANS': 226}
    Chain: "D"
      Number of atoms: 2235
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2235
          Classifications: {'peptide': 289}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 282}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1873  SG  CYS A 239      64.134  75.808  68.422  1.00 41.47           S
  ATOM   1892  SG  CYS A 242      60.387  80.594  66.157  1.00 35.22           S
  ATOM   1712  SG  CYS A 218      64.019  76.416  61.748  1.00 35.59           S

  Time building chain proxies: 2.21, per 1000 atoms: 0.27
  Number of scatterers: 8272
  At special positions: 0
  Unit cell: (94.2, 103.2, 108, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      48     16.00
     O    1583      8.00
     N    1393      7.00
     C    5244      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 382.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A 301 "
        pdb="FE1  SF4 A 301 " - pdb=" SG  CYS A 239 "
        pdb="FE4  SF4 A 301 " - pdb=" SG  CYS A 218 "
        pdb="FE3  SF4 A 301 " - pdb=" SG  CYS A 242 "
      Number of angles added : 9


  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1930

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      22.9% alpha, 39.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 54
      removed outlier: 3.849A  pdb=" N   ALA A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 83
      removed outlier: 3.803A  pdb=" N   MET A  83 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 104
    Processing helix  chain 'A' and resid 115 through 130
      removed outlier: 3.617A  pdb=" N   VAL A 130 " --> pdb=" O   ALA A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
      removed outlier: 3.648A  pdb=" N   TYR A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 163
      removed outlier: 3.513A  pdb=" N   LYS A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 195
      removed outlier: 3.677A  pdb=" N   VAL A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 209
      removed outlier: 3.766A  pdb=" N   ALA A 208 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 240
      removed outlier: 3.650A  pdb=" N   PHE A 234 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 296
    Processing helix  chain 'B' and resid 300 through 313
      removed outlier: 3.593A  pdb=" N   GLU B 306 " --> pdb=" O   ASP B 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 44 through 54
      removed outlier: 3.507A  pdb=" N   MET C  53 " --> pdb=" O   ALA C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 83
    Processing helix  chain 'C' and resid 99 through 104
    Processing helix  chain 'C' and resid 115 through 130
    Processing helix  chain 'C' and resid 133 through 138
      removed outlier: 3.511A  pdb=" N   TYR C 137 " --> pdb=" O   ASP C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 163
    Processing helix  chain 'C' and resid 181 through 194
      removed outlier: 3.621A  pdb=" N   ARG C 186 " --> pdb=" O   ASP C 182 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL C 187 " --> pdb=" O   GLU C 183 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS C 194 " --> pdb=" O   TYR C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 209
    Processing helix  chain 'C' and resid 227 through 237
      removed outlier: 4.415A  pdb=" N   GLU C 233 " --> pdb=" O   LYS C 229 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LYS C 237 " --> pdb=" O   GLU C 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 287 through 296
    Processing helix  chain 'D' and resid 300 through 313
      removed outlier: 3.509A  pdb=" N   ILE D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 29
      removed outlier: 6.536A  pdb=" N   VAL A  14 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LYS A  23 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   LEU A  12 " --> pdb=" O   LYS A  23 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL A  25 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   GLU A  10 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU A  27 " --> pdb=" O   LYS A   8 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   LYS A   8 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   LEU A  12 " --> pdb=" O   LYS A  62 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   LYS A  62 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   VAL A  14 " --> pdb=" O   PRO A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 88
      removed outlier: 6.752A  pdb=" N   THR A  86 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ASP A 170 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ALA A  88 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ALA A 167 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   ILE A 201 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU A 169 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE A  34 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   SER A 215 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ALA A  36 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   ILE A 217 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ILE A  38 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL A 214 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   SER A 225 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   LEU A 216 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 43
      removed outlier: 6.558A  pdb=" N   ILE B  33 " --> pdb=" O   ILE B  40 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   VAL B  42 " --> pdb=" O   ARG B  31 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ARG B  31 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   THR B 169 " --> pdb=" O   HIS B 138 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   HIS B 140 " --> pdb=" O   THR B 169 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   LYS B 170 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   ILE D 190 " --> pdb=" O   ILE D 220 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   LYS D 222 " --> pdb=" O   ILE D 190 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   ILE D 192 " --> pdb=" O   LYS D 222 " (cutoff:3.500A)
      removed outlier: 8.248A  pdb=" N   ARG D 224 " --> pdb=" O   ILE D 192 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   THR D 194 " --> pdb=" O   ARG D 224 " (cutoff:3.500A)
      removed outlier: 8.733A  pdb=" N   ALA D 226 " --> pdb=" O   THR D 194 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   THR D 196 " --> pdb=" O   ALA D 226 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   SER D 101 " --> pdb=" O   PHE D  71 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   TYR D  73 " --> pdb=" O   SER D 101 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   SER D 103 " --> pdb=" O   TYR D  73 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   ARG D  31 " --> pdb=" O   VAL D  42 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   VAL D  42 " --> pdb=" O   ARG D  31 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ILE D  33 " --> pdb=" O   ILE D  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 55
      removed outlier: 6.377A  pdb=" N   ILE B  59 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   GLU B  93 " --> pdb=" O   ILE B  59 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ALA B  61 " --> pdb=" O   GLU B  93 " (cutoff:3.500A)
      removed outlier: 8.514A  pdb=" N   ILE B  95 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE B  63 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   GLN B  88 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ASN B 121 " --> pdb=" O   GLN B  88 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ILE B  90 " --> pdb=" O   ASN B 121 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   ILE B 123 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   VAL B  92 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   LYS B 125 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE B  94 " --> pdb=" O   LYS B 125 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LYS B 114 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
      removed outlier: 8.781A  pdb=" N   LEU B 147 " --> pdb=" O   LYS B 114 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE B 116 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
      removed outlier: 8.270A  pdb=" N   LYS B 149 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   HIS B 118 " --> pdb=" O   LYS B 149 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   THR B 151 " --> pdb=" O   HIS B 118 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   MET B 120 " --> pdb=" O   THR B 151 " (cutoff:3.500A)
      removed outlier: 8.056A  pdb=" N   LYS B 153 " --> pdb=" O   MET B 120 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLY B 122 " --> pdb=" O   LYS B 153 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   GLU B 155 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ILE B 124 " --> pdb=" O   GLU B 155 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   LEU B 176 " --> pdb=" O   LYS B 205 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   ASN B 207 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ILE B 178 " --> pdb=" O   ASN B 207 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   VAL B 209 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   GLN B 180 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   LYS B 211 " --> pdb=" O   GLN B 180 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ILE B 182 " --> pdb=" O   LYS B 211 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   VAL B 204 " --> pdb=" O   SER B 234 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   LYS B 236 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   VAL B 206 " --> pdb=" O   LYS B 236 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   LYS B 238 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLU B 208 " --> pdb=" O   LYS B 238 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   GLU B 240 " --> pdb=" O   GLU B 208 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   VAL B 210 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   ILE B 233 " --> pdb=" O   GLU B 263 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   ILE B 265 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   LEU B 235 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   ILE B 267 " --> pdb=" O   LEU B 235 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   LEU B 237 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   VAL B 269 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE B 239 " --> pdb=" O   VAL B 269 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE D 233 " --> pdb=" O   GLU D 263 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   ILE D 265 " --> pdb=" O   ILE D 233 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU D 235 " --> pdb=" O   ILE D 265 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ILE D 267 " --> pdb=" O   LEU D 235 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   LEU D 237 " --> pdb=" O   ILE D 267 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   VAL D 269 " --> pdb=" O   LEU D 237 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   ILE D 239 " --> pdb=" O   VAL D 269 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   ILE D 146 " --> pdb=" O   THR D 175 " (cutoff:3.500A)
      removed outlier: 8.119A  pdb=" N   ASP D 177 " --> pdb=" O   ILE D 146 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL D 148 " --> pdb=" O   ASP D 177 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   GLU D 179 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   GLU D 181 " --> pdb=" O   PRO D 150 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL D 152 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
      removed outlier: 8.382A  pdb=" N   ILE D 183 " --> pdb=" O   VAL D 152 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL D 154 " --> pdb=" O   ILE D 183 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ILE D 116 " --> pdb=" O   LEU D 147 " (cutoff:3.500A)
      removed outlier: 8.152A  pdb=" N   LYS D 149 " --> pdb=" O   ILE D 116 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   HIS D 118 " --> pdb=" O   LYS D 149 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   THR D 151 " --> pdb=" O   HIS D 118 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   MET D 120 " --> pdb=" O   THR D 151 " (cutoff:3.500A)
      removed outlier: 8.222A  pdb=" N   LYS D 153 " --> pdb=" O   MET D 120 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   GLY D 122 " --> pdb=" O   LYS D 153 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   GLU D 155 " --> pdb=" O   GLY D 122 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   ILE D 124 " --> pdb=" O   GLU D 155 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   GLN D  88 " --> pdb=" O   ILE D 119 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   ASN D 121 " --> pdb=" O   GLN D  88 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE D  90 " --> pdb=" O   ASN D 121 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   ILE D 123 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   VAL D  92 " --> pdb=" O   ILE D 123 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   LYS D 125 " --> pdb=" O   VAL D  92 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ILE D  94 " --> pdb=" O   LYS D 125 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ILE D  59 " --> pdb=" O   ASP D  91 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   GLU D  93 " --> pdb=" O   ILE D  59 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   ALA D  61 " --> pdb=" O   GLU D  93 " (cutoff:3.500A)
      removed outlier: 8.321A  pdb=" N   ILE D  95 " --> pdb=" O   ALA D  61 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ILE D  63 " --> pdb=" O   ILE D  95 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 29
      removed outlier: 4.099A  pdb=" N   ARG C  19 " --> pdb=" O   ARG C  16 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL C  14 " --> pdb=" O   ILE C  21 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LYS C  23 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   LEU C  12 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   VAL C  25 " --> pdb=" O   GLU C  10 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   GLU C  10 " --> pdb=" O   VAL C  25 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU C  27 " --> pdb=" O   LYS C   8 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   LYS C   8 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LEU C  12 " --> pdb=" O   LYS C  62 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LYS C  62 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 88
      removed outlier: 3.645A  pdb=" N   ASP C 170 " --> pdb=" O   ALA C  88 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ALA C 167 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   ILE C 201 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   LEU C 169 " --> pdb=" O   ILE C 201 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ILE C  34 " --> pdb=" O   ARG C 213 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   SER C 215 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ALA C  36 " --> pdb=" O   SER C 215 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   ILE C 217 " --> pdb=" O   ALA C  36 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ILE C  38 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL C 214 " --> pdb=" O   SER C 225 " (cutoff:3.500A)
      removed outlier: 4.537A  pdb=" N   SER C 225 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU C 216 " --> pdb=" O   ILE C 223 " (cutoff:3.500A)

    346 hydrogen bonds defined for protein.
    1005 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: 1.60

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.21 -     1.43: 3260
        1.43 -     1.64: 5036
        1.64 -     1.86: 72
        1.86 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 8380
  Sorted by residual:
  bond pdb=" N   THR A  86 "
       pdb=" CA  THR A  86 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.25e-02 6.40e+03 8.86e+00
  bond pdb=" CA  ALA D 243 "
       pdb=" C   ALA D 243 "
    ideal  model  delta    sigma   weight residual
    1.519  1.547 -0.028 9.50e-03 1.11e+04 8.76e+00
  bond pdb=" CZ  ARG B 224 "
       pdb=" NH2 ARG B 224 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.60e+00
  bond pdb=" CA  GLU C 163 "
       pdb=" C   GLU C 163 "
    ideal  model  delta    sigma   weight residual
    1.531  1.553 -0.022 7.40e-03 1.83e+04 8.55e+00
  bond pdb=" N   ILE D 102 "
       pdb=" CA  ILE D 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.031 1.08e-02 8.57e+03 8.41e+00
  ... (remaining 8375 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 7636
        1.87 -     3.74: 2967
        3.74 -     5.61: 573
        5.61 -     7.48: 63
        7.48 -     9.35: 5
  Bond angle restraints: 11244
  Sorted by residual:
  angle pdb=" N   CYS D 219 "
        pdb=" CA  CYS D 219 "
        pdb=" C   CYS D 219 "
      ideal   model   delta    sigma   weight residual
     108.99  118.34   -9.35 1.57e+00 4.06e-01 3.55e+01
  angle pdb=" C   ASP B 272 "
        pdb=" N   ASP B 273 "
        pdb=" CA  ASP B 273 "
      ideal   model   delta    sigma   weight residual
     120.60  129.23   -8.63 1.60e+00 3.91e-01 2.91e+01
  angle pdb=" CA  ASP A 227 "
        pdb=" CB  ASP A 227 "
        pdb=" CG  ASP A 227 "
      ideal   model   delta    sigma   weight residual
     112.60  117.93   -5.33 1.00e+00 1.00e+00 2.84e+01
  angle pdb=" CA  PHE A 188 "
        pdb=" CB  PHE A 188 "
        pdb=" CG  PHE A 188 "
      ideal   model   delta    sigma   weight residual
     113.80  119.02   -5.22 1.00e+00 1.00e+00 2.73e+01
  angle pdb=" C   ALA D 243 "
        pdb=" N   PRO D 244 "
        pdb=" CA  PRO D 244 "
      ideal   model   delta    sigma   weight residual
     119.90  125.15   -5.25 1.02e+00 9.61e-01 2.65e+01
  ... (remaining 11239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 4775
       17.23 -    34.46: 308
       34.46 -    51.68: 76
       51.68 -    68.91: 32
       68.91 -    86.14: 7
  Dihedral angle restraints: 5198
    sinusoidal: 2183
      harmonic: 3015
  Sorted by residual:
  dihedral pdb=" CA  ILE D 190 "
           pdb=" C   ILE D 190 "
           pdb=" N   ASP D 191 "
           pdb=" CA  ASP D 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  ASP B 143 "
           pdb=" C   ASP B 143 "
           pdb=" N   GLY B 144 "
           pdb=" CA  GLY B 144 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.65   22.35     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" C   ASN B 259 "
           pdb=" N   ASN B 259 "
           pdb=" CA  ASN B 259 "
           pdb=" CB  ASN B 259 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.74   11.14     0      2.50e+00 1.60e-01 1.99e+01
  ... (remaining 5195 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 708
       0.075 -    0.150: 413
       0.150 -    0.225: 127
       0.225 -    0.300: 28
       0.300 -    0.376: 12
  Chirality restraints: 1288
  Sorted by residual:
  chirality pdb=" CA  TYR B 245 "
            pdb=" N   TYR B 245 "
            pdb=" C   TYR B 245 "
            pdb=" CB  TYR B 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.53e+00
  chirality pdb=" CA  ASN B 259 "
            pdb=" N   ASN B 259 "
            pdb=" C   ASN B 259 "
            pdb=" CB  ASN B 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.00e+00
  chirality pdb=" CA  TYR D 245 "
            pdb=" N   TYR D 245 "
            pdb=" C   TYR D 245 "
            pdb=" CB  TYR D 245 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.87e+00
  ... (remaining 1285 not shown)

  Planarity restraints: 1427
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 139 "   -0.097 2.00e-02 2.50e+03   5.31e-02 5.64e+01
        pdb=" CG  TYR B 139 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 139 "    0.037 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 139 "    0.049 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 139 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 139 "    0.022 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 139 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 139 "   -0.081 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 245 "   -0.095 2.00e-02 2.50e+03   5.07e-02 5.14e+01
        pdb=" CG  TYR B 245 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 245 "    0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 245 "    0.042 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 245 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 245 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 245 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 245 "   -0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 181 "   -0.080 2.00e-02 2.50e+03   4.89e-02 4.19e+01
        pdb=" CG  PHE A 181 "    0.060 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 181 "    0.046 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 181 "    0.045 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 181 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 181 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 181 "   -0.047 2.00e-02 2.50e+03
  ... (remaining 1424 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 3709
        3.02 -     3.49: 7209
        3.49 -     3.96: 12543
        3.96 -     4.43: 13163
        4.43 -     4.90: 24012
  Nonbonded interactions: 60636
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 112 "
            pdb=" OE1 GLU C 163 "
     model   vdw
     2.549 3.040
  nonbonded pdb=" OH  TYR A 112 "
            pdb=" OE1 GLU A 163 "
     model   vdw
     2.568 3.040
  nonbonded pdb=" OG  SER C  56 "
            pdb=" OE2 GLU D 292 "
     model   vdw
     2.574 3.040
  nonbonded pdb=" OG  SER A  56 "
            pdb=" OE2 GLU B 292 "
     model   vdw
     2.577 3.040
  nonbonded pdb=" OG  SER C 147 "
            pdb=" OE1 GLU C 150 "
     model   vdw
     2.577 3.040
  ... (remaining 60631 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 4 through 237)
  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 individual isotropic
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:             5.600
  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:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.230
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
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      :  0.014   0.375   8383  Z= 0.888
  Angle     :  1.947   9.443  11253  Z= 1.287
  Chirality :  0.102   0.376   1288
  Planarity :  0.012   0.098   1427
  Dihedral  : 13.769  86.140   3268
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 0.06
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  1.72 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.50 %
    Favored  : 92.39 %
  Cbeta Deviations :  0.21 %
  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:  0.21 (0.24), residues: 1048
  helix: -1.44 (0.28), residues: 220
  sheet:  2.13 (0.24), residues: 408
  loop : -1.02 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 151 
 TYR   0.097   0.016   TYR B 139 
 PHE   0.080   0.010   PHE A 181 
 TRP   0.038   0.016   TRP A  89 
 HIS   0.011   0.004   HIS B 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.01357 ( 8380)
  covalent geometry    : angle       1.94140 (11244)
  hydrogen bonds       : bond        0.25234 (  346)
  hydrogen bonds       : angle       7.30755 ( 1005)
  metal coordination   : bond        0.25147 (    3)
  metal coordination   : angle       5.44764 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 196
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6807 (mmm-85) cc_final: 0.5665 (tpp80)
REVERT: A  124 ARG cc_start: 0.7154 (mtp85) cc_final: 0.6787 (mtt90)
REVERT: B   33 ILE cc_start: 0.7958 (mt) cc_final: 0.7709 (mm)
REVERT: B   37 SER cc_start: 0.6665 (t) cc_final: 0.6348 (p)
REVERT: C   80 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8068 (mtt180)
REVERT: C  224 LYS cc_start: 0.7573 (tttm) cc_final: 0.6979 (ttpp)
REVERT: D   43 GLN cc_start: 0.5760 (tt0) cc_final: 0.5298 (tt0)
REVERT: D   69 TYR cc_start: 0.6591 (m-80) cc_final: 0.5788 (m-80)
REVERT: D  117 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7113 (mptt)
  outliers start: 10
  outliers final: 3
  residues processed: 204
  average time/residue: 0.6860
  time to fit residues: 146.9099
Evaluate side-chains
  135 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   80 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0170
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
B 118 HIS
B 138 HIS
C  13 HIS
C  32 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.162954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.133745 restraints weight = 9498.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.70
r_work: 0.3519 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8383  Z= 0.195
  Angle     :  0.668   7.512  11253  Z= 0.378
  Chirality :  0.051   0.160   1288
  Planarity :  0.004   0.062   1427
  Dihedral  :  5.647  52.352   1135
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 12.68 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.89 (0.25), residues: 1048
  helix:  0.34 (0.32), residues: 238
  sheet:  1.41 (0.23), residues: 451
  loop : -0.22 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  82 
 TYR   0.018   0.001   TYR C  15 
 PHE   0.013   0.002   PHE D 137 
 TRP   0.006   0.002   TRP A  89 
 HIS   0.004   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8380)
  covalent geometry    : angle       0.65180 (11244)
  hydrogen bonds       : bond        0.06214 (  346)
  hydrogen bonds       : angle       5.07384 ( 1005)
  metal coordination   : bond        0.00623 (    3)
  metal coordination   : angle       5.20473 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6338 (mmm-85) cc_final: 0.5270 (tpp80)
REVERT: A  199 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (tt)
REVERT: A  230 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7110 (tm-30)
REVERT: B  261 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8229 (tt0)
REVERT: C   26 ASN cc_start: 0.8032 (t0) cc_final: 0.7653 (m-40)
REVERT: C  171 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7407 (mm-30)
REVERT: D   43 GLN cc_start: 0.5935 (tt0) cc_final: 0.5346 (tt0)
REVERT: D  117 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7349 (mptt)
REVERT: D  195 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7108 (mtp180)
REVERT: D  288 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7916 (ttmm)
  outliers start: 31
  outliers final: 8
  residues processed: 173
  average time/residue: 0.6606
  time to fit residues: 120.4330
Evaluate side-chains
  134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  259 ASN
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain D residue  145 ASP
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  220 ILE
Chi-restraints excluded: chain D residue  288 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.156155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.125997 restraints weight = 9338.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.69
r_work: 0.3402 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8383  Z= 0.250
  Angle     :  0.768  10.218  11253  Z= 0.429
  Chirality :  0.055   0.203   1288
  Planarity :  0.005   0.083   1427
  Dihedral  :  5.491  55.413   1130
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 15.21 %
    Favored  : 79.82 %
  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:  0.68 (0.25), residues: 1048
  helix:  0.49 (0.34), residues: 232
  sheet:  1.23 (0.23), residues: 447
  loop : -0.48 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 224 
 TYR   0.020   0.002   TYR C  15 
 PHE   0.015   0.002   PHE B  71 
 TRP   0.011   0.003   TRP C  89 
 HIS   0.005   0.002   HIS C 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 8380)
  covalent geometry    : angle       0.75036 (11244)
  hydrogen bonds       : bond        0.07790 (  346)
  hydrogen bonds       : angle       5.15067 ( 1005)
  metal coordination   : bond        0.01892 (    3)
  metal coordination   : angle       5.76827 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 121
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6399 (mmm-85) cc_final: 0.5243 (tpp80)
REVERT: A  199 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8635 (tt)
REVERT: A  230 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7168 (tm-30)
REVERT: A  233 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7954 (mt-10)
REVERT: B   31 ARG cc_start: 0.6605 (ptp90) cc_final: 0.6370 (ptp90)
REVERT: B   51 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6956 (pt0)
REVERT: C   80 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7843 (mtt180)
REVERT: C  171 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7153 (mm-30)
REVERT: D   43 GLN cc_start: 0.5898 (tt0) cc_final: 0.5532 (tt0)
REVERT: D  117 LYS cc_start: 0.7991 (mmmm) cc_final: 0.7399 (mptt)
REVERT: D  181 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6975 (tm-30)
REVERT: D  195 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7286 (mtp180)
REVERT: D  288 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7902 (ttmm)
  outliers start: 45
  outliers final: 13
  residues processed: 149
  average time/residue: 0.6825
  time to fit residues: 107.0203
Evaluate side-chains
  143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain B residue   51 GLU
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   80 ARG
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  288 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0050
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.7800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.155295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125121 restraints weight = 9477.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.71
r_work: 0.3403 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8383  Z= 0.239
  Angle     :  0.741  10.070  11253  Z= 0.411
  Chirality :  0.054   0.184   1288
  Planarity :  0.005   0.082   1427
  Dihedral  :  5.397  48.235   1130
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 16.54 %
    Favored  : 77.95 %
  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:  0.56 (0.25), residues: 1048
  helix:  0.69 (0.34), residues: 226
  sheet:  1.03 (0.24), residues: 451
  loop : -0.59 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  82 
 TYR   0.019   0.002   TYR C  15 
 PHE   0.013   0.002   PHE B  71 
 TRP   0.011   0.003   TRP C  89 
 HIS   0.004   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 8380)
  covalent geometry    : angle       0.72381 (11244)
  hydrogen bonds       : bond        0.07527 (  346)
  hydrogen bonds       : angle       5.05934 ( 1005)
  metal coordination   : bond        0.01820 (    3)
  metal coordination   : angle       5.66063 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 124
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6424 (mmm-85) cc_final: 0.5306 (tpp80)
REVERT: A  229 LYS cc_start: 0.7530 (tmmt) cc_final: 0.6978 (mmtm)
REVERT: A  230 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7200 (tm-30)
REVERT: A  233 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7942 (mt-10)
REVERT: B   67 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7981 (ttmm)
REVERT: B  112 LYS cc_start: 0.7273 (tmtm) cc_final: 0.6994 (ptmm)
REVERT: B  155 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7960 (mp0)
REVERT: C   55 ILE cc_start: 0.8114 (OUTLIER) cc_final: 0.7285 (mp)
REVERT: C   80 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7826 (mtt180)
REVERT: D   43 GLN cc_start: 0.5900 (tt0) cc_final: 0.5544 (tt0)
REVERT: D   83 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6941 (pp20)
REVERT: D   86 ILE cc_start: 0.7920 (mm) cc_final: 0.7562 (mt)
REVERT: D  117 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7373 (mptt)
REVERT: D  181 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6974 (tm-30)
REVERT: D  195 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7368 (mtp180)
REVERT: D  288 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7914 (ttmm)
  outliers start: 50
  outliers final: 17
  residues processed: 156
  average time/residue: 0.6561
  time to fit residues: 107.9977
Evaluate side-chains
  144 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain B residue   67 LYS
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   80 ARG
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  288 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0870
   chunk 78 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.1564

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.157248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.127541 restraints weight = 9418.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.70
r_work: 0.3434 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8383  Z= 0.188
  Angle     :  0.651   8.953  11253  Z= 0.361
  Chirality :  0.052   0.175   1288
  Planarity :  0.005   0.079   1427
  Dihedral  :  5.061  38.905   1130
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 17.42 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1048
  helix:  1.06 (0.34), residues: 226
  sheet:  0.96 (0.24), residues: 453
  loop : -0.58 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  31 
 TYR   0.018   0.001   TYR C  15 
 PHE   0.029   0.002   PHE C 234 
 TRP   0.009   0.002   TRP C  89 
 HIS   0.004   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8380)
  covalent geometry    : angle       0.63241 (11244)
  hydrogen bonds       : bond        0.06432 (  346)
  hydrogen bonds       : angle       4.81305 ( 1005)
  metal coordination   : bond        0.01457 (    3)
  metal coordination   : angle       5.46403 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 127
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6450 (mmm-85) cc_final: 0.5358 (tpp80)
REVERT: A  230 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7200 (tm-30)
REVERT: A  233 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7944 (mt-10)
REVERT: B  155 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7927 (mt-10)
REVERT: B  261 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8049 (mp0)
REVERT: C   55 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7211 (mp)
REVERT: C   80 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7775 (mtt180)
REVERT: D   31 ARG cc_start: 0.6840 (ptp90) cc_final: 0.6503 (ptp90)
REVERT: D   43 GLN cc_start: 0.5895 (tt0) cc_final: 0.5592 (tt0)
REVERT: D   83 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6890 (pp20)
REVERT: D   86 ILE cc_start: 0.7889 (mm) cc_final: 0.7554 (mt)
REVERT: D  117 LYS cc_start: 0.7994 (mmmm) cc_final: 0.7341 (mptt)
REVERT: D  170 LYS cc_start: 0.8190 (mttm) cc_final: 0.7920 (mttp)
REVERT: D  181 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6911 (tm-30)
REVERT: D  195 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7304 (mtp180)
REVERT: D  288 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7879 (ttmm)
  outliers start: 48
  outliers final: 22
  residues processed: 162
  average time/residue: 0.6395
  time to fit residues: 109.3461
Evaluate side-chains
  151 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 119
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   80 ARG
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  288 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0470
   chunk 87 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.9682

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.158088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.128715 restraints weight = 9434.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.69
r_work: 0.3457 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8383  Z= 0.169
  Angle     :  0.617   8.808  11253  Z= 0.341
  Chirality :  0.051   0.204   1288
  Planarity :  0.005   0.078   1427
  Dihedral  :  4.832  32.641   1130
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 17.86 %
    Favored  : 76.63 %
  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:  0.75 (0.26), residues: 1048
  helix:  1.28 (0.35), residues: 224
  sheet:  0.97 (0.24), residues: 453
  loop : -0.53 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  31 
 TYR   0.017   0.001   TYR C  15 
 PHE   0.023   0.002   PHE C 234 
 TRP   0.007   0.002   TRP C  89 
 HIS   0.004   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8380)
  covalent geometry    : angle       0.59795 (11244)
  hydrogen bonds       : bond        0.05911 (  346)
  hydrogen bonds       : angle       4.67347 ( 1005)
  metal coordination   : bond        0.01316 (    3)
  metal coordination   : angle       5.37698 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 123
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6435 (mmm-85) cc_final: 0.5372 (tpp80)
REVERT: A  183 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6860 (tm-30)
REVERT: A  230 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7151 (tm-30)
REVERT: A  233 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7926 (mt-10)
REVERT: B   43 GLN cc_start: 0.6641 (tm-30) cc_final: 0.5753 (tt0)
REVERT: B   67 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7941 (ttmm)
REVERT: B   75 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6955 (mt)
REVERT: B  155 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7829 (mp0)
REVERT: B  261 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8067 (mp0)
REVERT: B  302 ASP cc_start: 0.8505 (m-30) cc_final: 0.8269 (m-30)
REVERT: C   55 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7188 (mp)
REVERT: C  224 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7219 (ttpp)
REVERT: D   31 ARG cc_start: 0.6701 (ptp90) cc_final: 0.6362 (ptp90)
REVERT: D   43 GLN cc_start: 0.5891 (tt0) cc_final: 0.5548 (tt0)
REVERT: D   83 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6967 (pp20)
REVERT: D   86 ILE cc_start: 0.7878 (mm) cc_final: 0.7571 (mt)
REVERT: D  170 LYS cc_start: 0.8135 (mttm) cc_final: 0.7736 (mmtm)
REVERT: D  181 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6907 (tm-30)
REVERT: D  195 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7265 (mtp180)
REVERT: D  233 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8526 (mp)
REVERT: D  288 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7863 (ttmm)
  outliers start: 50
  outliers final: 24
  residues processed: 157
  average time/residue: 0.6267
  time to fit residues: 104.0296
Evaluate side-chains
  156 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 119
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain B residue   67 LYS
Chi-restraints excluded: chain B residue   75 ILE
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   98 GLU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  192 ILE
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  288 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 98 optimal weight:    0.3980
   chunk 32 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.8186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.155343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.125328 restraints weight = 9406.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.73
r_work: 0.3417 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8383  Z= 0.236
  Angle     :  0.720  10.167  11253  Z= 0.397
  Chirality :  0.054   0.196   1288
  Planarity :  0.005   0.082   1427
  Dihedral  :  5.168  36.373   1130
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 18.19 %
    Favored  : 76.19 %
  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:  0.54 (0.26), residues: 1048
  helix:  1.02 (0.35), residues: 226
  sheet:  0.94 (0.24), residues: 453
  loop : -0.74 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  31 
 TYR   0.018   0.002   TYR C  15 
 PHE   0.020   0.002   PHE C 234 
 TRP   0.009   0.003   TRP C  89 
 HIS   0.004   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 8380)
  covalent geometry    : angle       0.70231 (11244)
  hydrogen bonds       : bond        0.07353 (  346)
  hydrogen bonds       : angle       4.95176 ( 1005)
  metal coordination   : bond        0.01810 (    3)
  metal coordination   : angle       5.66743 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 120
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6447 (mmm-85) cc_final: 0.5350 (tpp80)
REVERT: A  230 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7217 (tm-30)
REVERT: A  233 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7955 (mt-10)
REVERT: B   67 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8011 (ttmm)
REVERT: B  155 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7982 (mp0)
REVERT: B  261 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8013 (mp0)
REVERT: C   55 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7191 (mp)
REVERT: C   80 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7815 (mtt180)
REVERT: C  221 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6025 (tp30)
REVERT: C  224 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7223 (ttpp)
REVERT: D   31 ARG cc_start: 0.6786 (ptp90) cc_final: 0.6450 (ptp90)
REVERT: D   43 GLN cc_start: 0.5912 (tt0) cc_final: 0.5614 (tt0)
REVERT: D   83 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.7014 (pp20)
REVERT: D   86 ILE cc_start: 0.7841 (mm) cc_final: 0.7560 (mt)
REVERT: D  170 LYS cc_start: 0.8179 (mttm) cc_final: 0.7955 (mttp)
REVERT: D  181 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7051 (tm-30)
REVERT: D  195 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7361 (mtp180)
REVERT: D  233 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8608 (mp)
REVERT: D  288 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7910 (ttmm)
REVERT: D  310 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8270 (mtmm)
  outliers start: 51
  outliers final: 27
  residues processed: 154
  average time/residue: 0.6267
  time to fit residues: 102.1299
Evaluate side-chains
  159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 118
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  237 LYS
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain B residue   67 LYS
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  100 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  142 MET
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   80 ARG
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   98 GLU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  182 ILE
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  288 LYS
Chi-restraints excluded: chain D residue  310 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 53 optimal weight:    0.2980
   chunk 82 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0670
   chunk 9 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6724

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.160293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.131081 restraints weight = 9422.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.72
r_work: 0.3497 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3380 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.3585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8383  Z= 0.144
  Angle     :  0.574   7.806  11253  Z= 0.317
  Chirality :  0.050   0.175   1288
  Planarity :  0.004   0.075   1427
  Dihedral  :  4.656  28.591   1130
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 19.18 %
    Favored  : 76.19 %
  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:  0.80 (0.26), residues: 1048
  helix:  1.45 (0.35), residues: 223
  sheet:  0.99 (0.24), residues: 453
  loop : -0.58 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  31 
 TYR   0.016   0.001   TYR C  15 
 PHE   0.019   0.001   PHE C 234 
 TRP   0.006   0.001   TRP A  89 
 HIS   0.003   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8380)
  covalent geometry    : angle       0.55514 (11244)
  hydrogen bonds       : bond        0.05240 (  346)
  hydrogen bonds       : angle       4.54661 ( 1005)
  metal coordination   : bond        0.01060 (    3)
  metal coordination   : angle       5.21620 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6461 (mmm-85) cc_final: 0.5388 (tpp80)
REVERT: A  183 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6813 (tm-30)
REVERT: A  230 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7112 (tm-30)
REVERT: A  233 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7925 (mt-10)
REVERT: B  105 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7212 (mmm)
REVERT: B  139 TYR cc_start: 0.6644 (m-80) cc_final: 0.6183 (m-80)
REVERT: B  261 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8083 (mp0)
REVERT: C   55 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7125 (mp)
REVERT: C   80 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7729 (mtt180)
REVERT: D   31 ARG cc_start: 0.6637 (ptp90) cc_final: 0.6362 (ptp90)
REVERT: D   43 GLN cc_start: 0.5893 (tt0) cc_final: 0.5641 (tt0)
REVERT: D   83 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7127 (pp20)
REVERT: D   86 ILE cc_start: 0.7807 (mm) cc_final: 0.7535 (mt)
REVERT: D  170 LYS cc_start: 0.8156 (mttm) cc_final: 0.7758 (mmtm)
REVERT: D  181 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6911 (tm-30)
REVERT: D  195 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7184 (mtp180)
REVERT: D  233 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8501 (mp)
REVERT: D  288 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7896 (ttmm)
REVERT: D  310 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8202 (mtmm)
  outliers start: 42
  outliers final: 22
  residues processed: 150
  average time/residue: 0.6061
  time to fit residues: 96.2495
Evaluate side-chains
  147 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   80 ARG
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   98 GLU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  288 LYS
Chi-restraints excluded: chain D residue  310 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.159715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.130282 restraints weight = 9429.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 1.71
r_work: 0.3486 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8383  Z= 0.155
  Angle     :  0.589   8.453  11253  Z= 0.324
  Chirality :  0.051   0.190   1288
  Planarity :  0.004   0.077   1427
  Dihedral  :  4.618  28.297   1130
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 20.07 %
    Favored  : 75.63 %
  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:  0.84 (0.26), residues: 1048
  helix:  1.47 (0.35), residues: 226
  sheet:  1.05 (0.24), residues: 451
  loop : -0.60 (0.31), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  31 
 TYR   0.016   0.001   TYR C  15 
 PHE   0.017   0.002   PHE C 234 
 TRP   0.006   0.002   TRP C  89 
 HIS   0.003   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8380)
  covalent geometry    : angle       0.57016 (11244)
  hydrogen bonds       : bond        0.05487 (  346)
  hydrogen bonds       : angle       4.55847 ( 1005)
  metal coordination   : bond        0.01194 (    3)
  metal coordination   : angle       5.27800 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 120
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6450 (mmm-85) cc_final: 0.5376 (tpp80)
REVERT: A  183 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6809 (tm-30)
REVERT: A  230 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7123 (tm-30)
REVERT: A  233 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7921 (mt-10)
REVERT: B  105 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7225 (mmm)
REVERT: B  139 TYR cc_start: 0.6691 (m-80) cc_final: 0.6218 (m-80)
REVERT: B  261 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8122 (mp0)
REVERT: C   55 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7166 (mp)
REVERT: C   80 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7729 (mtt180)
REVERT: C  224 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7262 (ttpp)
REVERT: D   31 ARG cc_start: 0.6623 (ptp90) cc_final: 0.6344 (ptp90)
REVERT: D   43 GLN cc_start: 0.5894 (tt0) cc_final: 0.5618 (tt0)
REVERT: D   83 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7165 (pp20)
REVERT: D   86 ILE cc_start: 0.7822 (mm) cc_final: 0.7555 (mt)
REVERT: D  170 LYS cc_start: 0.8145 (mttm) cc_final: 0.7749 (mmtm)
REVERT: D  181 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6931 (tm-30)
REVERT: D  195 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7231 (mtp180)
REVERT: D  233 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8510 (mp)
REVERT: D  288 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7877 (ttmm)
REVERT: D  310 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8206 (mtmm)
  outliers start: 39
  outliers final: 22
  residues processed: 145
  average time/residue: 0.6782
  time to fit residues: 103.7322
Evaluate side-chains
  149 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   80 ARG
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue   83 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   98 GLU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  288 LYS
Chi-restraints excluded: chain D residue  310 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 89 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.2582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.157720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.127859 restraints weight = 9328.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.72
r_work: 0.3454 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8383  Z= 0.192
  Angle     :  0.652   9.796  11253  Z= 0.358
  Chirality :  0.052   0.213   1288
  Planarity :  0.005   0.079   1427
  Dihedral  :  4.818  30.830   1130
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 20.18 %
    Favored  : 75.63 %
  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:  0.75 (0.26), residues: 1048
  helix:  1.36 (0.35), residues: 223
  sheet:  1.02 (0.24), residues: 451
  loop : -0.65 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  31 
 TYR   0.016   0.001   TYR C  15 
 PHE   0.016   0.002   PHE C 234 
 TRP   0.007   0.002   TRP C  89 
 HIS   0.004   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8380)
  covalent geometry    : angle       0.63332 (11244)
  hydrogen bonds       : bond        0.06382 (  346)
  hydrogen bonds       : angle       4.73472 ( 1005)
  metal coordination   : bond        0.01520 (    3)
  metal coordination   : angle       5.56391 (    9)

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 ARG cc_start: 0.6467 (mmm-85) cc_final: 0.5374 (tpp80)
REVERT: A  183 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6892 (tm-30)
REVERT: A  230 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7172 (tm-30)
REVERT: A  233 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7913 (mt-10)
REVERT: B  105 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7271 (mmm)
REVERT: B  261 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8059 (mp0)
REVERT: C   55 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7165 (mp)
REVERT: C   80 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7787 (mtt180)
REVERT: C  224 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7262 (ttpp)
REVERT: D   31 ARG cc_start: 0.6686 (ptp90) cc_final: 0.6472 (ptp90)
REVERT: D   43 GLN cc_start: 0.5877 (tt0) cc_final: 0.5603 (tt0)
REVERT: D   86 ILE cc_start: 0.7835 (mm) cc_final: 0.7582 (mt)
REVERT: D  170 LYS cc_start: 0.8144 (mttm) cc_final: 0.7745 (mtpm)
REVERT: D  181 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6989 (tm-30)
REVERT: D  195 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7322 (mtp180)
REVERT: D  233 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: D  288 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7882 (ttmm)
REVERT: D  310 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8216 (mtmm)
  outliers start: 38
  outliers final: 22
  residues processed: 143
  average time/residue: 0.6669
  time to fit residues: 100.6561
Evaluate side-chains
  151 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  230 GLU
Chi-restraints excluded: chain A residue  233 GLU
Chi-restraints excluded: chain A residue  246 VAL
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  104 LEU
Chi-restraints excluded: chain B residue  105 MET
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  120 MET
Chi-restraints excluded: chain B residue  153 LYS
Chi-restraints excluded: chain B residue  232 LYS
Chi-restraints excluded: chain B residue  261 GLU
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   21 ILE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue   80 ARG
Chi-restraints excluded: chain C residue  139 ASP
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  224 LYS
Chi-restraints excluded: chain D residue   75 ILE
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   98 GLU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  120 MET
Chi-restraints excluded: chain D residue  181 GLU
Chi-restraints excluded: chain D residue  195 ARG
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  288 LYS
Chi-restraints excluded: chain D residue  310 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0010
   chunk 77 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.0790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.158362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.128703 restraints weight = 9431.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.72
r_work: 0.3466 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8383  Z= 0.176
  Angle     :  0.629   9.070  11253  Z= 0.346
  Chirality :  0.051   0.209   1288
  Planarity :  0.005   0.077   1427
  Dihedral  :  4.743  29.861   1130
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 19.63 %
    Favored  : 75.63 %
  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:  0.78 (0.26), residues: 1048
  helix:  1.42 (0.35), residues: 223
  sheet:  1.03 (0.24), residues: 451
  loop : -0.64 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  31 
 TYR   0.016   0.001   TYR C  15 
 PHE   0.017   0.002   PHE C 234 
 TRP   0.007   0.002   TRP C  89 
 HIS   0.004   0.001   HIS D 279 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8380)
  covalent geometry    : angle       0.61011 (11244)
  hydrogen bonds       : bond        0.06000 (  346)
  hydrogen bonds       : angle       4.66881 ( 1005)
  metal coordination   : bond        0.01377 (    3)
  metal coordination   : angle       5.40766 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3694.46 seconds
wall clock time: 63 minutes 30.49 seconds (3810.49 seconds total)