Starting phenix.real_space_refine
on Wed Mar  4 07:33:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7o12_12687/03_2026/7o12_12687.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7o12_12687/03_2026/7o12_12687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7o12_12687/03_2026/7o12_12687.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7o12_12687/03_2026/7o12_12687.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7o12_12687/03_2026/7o12_12687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7o12_12687/03_2026/7o12_12687.map"
  }
  resolution = 3.7
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      3      5.21       5
     S      36      5.16       5
     C    7471      2.51       5
     N    2047      2.21       5
     O    2128      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11691
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2295
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 12, 'TRANS': 285}
    Chain: "C"
      Number of atoms: 2295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2295
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 12, 'TRANS': 285}
    Chain: "A"
      Number of atoms: 3140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 3140
          Classifications: {'peptide': 402}
          Link IDs: {'PTRANS': 16, 'TRANS': 385}
    Chain: "E"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 1880
          Classifications: {'peptide': 246}
          Link IDs: {'PTRANS': 8, 'TRANS': 237}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 2015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 267, 2015
          Classifications: {'peptide': 267}
          Link IDs: {'PTRANS': 8, 'TRANS': 258}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 2.82, per 1000 atoms: 0.24
  Number of scatterers: 11691
  At special positions: 0
  Unit cell: (83.106, 168.264, 134.406, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       6     15.00
     Mg      3     11.99
     O    2128      8.00
     N    2047      7.00
     C    7471      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: 0.87
  Conformation dependent library (CDL) restraints added in 617.6 milliseconds
  

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2716

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 14 sheets defined
      48.2% alpha, 11.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 41 through 51
      removed outlier: 3.532A  pdb=" N   MET B  46 " --> pdb=" O   LYS B  42 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE B  49 " --> pdb=" O   SER B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 90 through 103
      removed outlier: 3.707A  pdb=" N   LEU B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 3.777A  pdb=" N   LEU B 112 " --> pdb=" O   GLN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 129
    Processing helix  chain 'B' and resid 130 through 143
      removed outlier: 4.001A  pdb=" N   ALA B 142 " --> pdb=" O   GLY B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 177
      removed outlier: 3.530A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 192
      removed outlier: 4.094A  pdb=" N   VAL B 191 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLU B 192 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 187 through 192'
    Processing helix  chain 'B' and resid 211 through 219
    Processing helix  chain 'B' and resid 237 through 242
      removed outlier: 3.784A  pdb=" N   THR B 241 " --> pdb=" O   LEU B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 274
    Processing helix  chain 'B' and resid 286 through 299
      removed outlier: 3.776A  pdb=" N   GLU B 296 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA B 298 " --> pdb=" O   TYR B 294 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 51
      removed outlier: 3.563A  pdb=" N   MET C  46 " --> pdb=" O   LYS C  42 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 76
      removed outlier: 3.671A  pdb=" N   LEU C  76 " --> pdb=" O   ARG C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 103
      removed outlier: 3.572A  pdb=" N   LEU C  95 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 107 through 117
      removed outlier: 4.741A  pdb=" N   GLU C 111 " --> pdb=" O   THR C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 129
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 177
    Processing helix  chain 'C' and resid 190 through 194
      removed outlier: 3.635A  pdb=" N   ALA C 193 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 211 through 219
    Processing helix  chain 'C' and resid 237 through 242
      removed outlier: 3.775A  pdb=" N   THR C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 263 through 274
    Processing helix  chain 'C' and resid 286 through 299
      removed outlier: 3.560A  pdb=" N   MET C 295 " --> pdb=" O   TYR C 291 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   GLU C 296 " --> pdb=" O   ARG C 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 34
    Processing helix  chain 'A' and resid 375 through 383
      removed outlier: 3.516A  pdb=" N   LEU A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   TRP A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 390
    Processing helix  chain 'A' and resid 392 through 405
      removed outlier: 3.503A  pdb=" N   GLN A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 7
    Processing helix  chain 'E' and resid 7 through 16
      removed outlier: 3.652A  pdb=" N   GLU E  11 " --> pdb=" O   ILE E   7 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 41
      removed outlier: 3.527A  pdb=" N   ILE E  24 " --> pdb=" O   TRP E  20 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA E  36 " --> pdb=" O   ALA E  32 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 52 through 75
      removed outlier: 3.817A  pdb=" N   SER E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      Proline residue:  E  67  - end of helix
    Processing helix  chain 'E' and resid 78 through 84
    Processing helix  chain 'E' and resid 85 through 91
      removed outlier: 3.575A  pdb=" N   LEU E  89 " --> pdb=" O   GLY E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 96 through 120
      removed outlier: 3.633A  pdb=" N   ILE E 111 " --> pdb=" O   GLY E 107 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU E 112 " --> pdb=" O   HIS E 108 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU E 117 " --> pdb=" O   ALA E 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 129
    Processing helix  chain 'E' and resid 138 through 143
    Processing helix  chain 'E' and resid 143 through 168
      removed outlier: 3.593A  pdb=" N   SER E 149 " --> pdb=" O   ARG E 145 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 170 through 188
      removed outlier: 3.507A  pdb=" N   GLY E 180 " --> pdb=" O   GLY E 176 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL E 188 " --> pdb=" O   LEU E 184 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 199
    Processing helix  chain 'E' and resid 208 through 213
      removed outlier: 3.535A  pdb=" N   LEU E 213 " --> pdb=" O   LEU E 209 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 216 through 224
    Processing helix  chain 'E' and resid 248 through 272
      removed outlier: 3.815A  pdb=" N   LEU E 252 " --> pdb=" O   PRO E 248 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER E 263 " --> pdb=" O   TRP E 259 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 16
      removed outlier: 4.049A  pdb=" N   LYS D  10 " --> pdb=" O   ASN D   6 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU D  11 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU D  16 " --> pdb=" O   LEU D  12 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 18 through 42
      removed outlier: 3.524A  pdb=" N   ILE D  24 " --> pdb=" O   TRP D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 75
      removed outlier: 3.743A  pdb=" N   ALA D  56 " --> pdb=" O   PRO D  52 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU D  58 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      Proline residue:  D  67  - end of helix
      removed outlier: 3.538A  pdb=" N   TYR D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 83
    Processing helix  chain 'D' and resid 85 through 91
      removed outlier: 3.794A  pdb=" N   LEU D  89 " --> pdb=" O   GLY D  85 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 129
      removed outlier: 3.914A  pdb=" N   LYS D 104 " --> pdb=" O   ILE D 100 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE D 111 " --> pdb=" O   GLY D 107 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU D 129 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 167
      removed outlier: 3.591A  pdb=" N   SER D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   LEU D 152 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 188
      removed outlier: 3.560A  pdb=" N   GLY D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL D 188 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 201
    Processing helix  chain 'D' and resid 208 through 215
    Processing helix  chain 'D' and resid 216 through 226
    Processing helix  chain 'D' and resid 232 through 237
      removed outlier: 3.834A  pdb=" N   MET D 236 " --> pdb=" O   SER D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 238 through 244
      removed outlier: 4.017A  pdb=" N   ALA D 243 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 272
      removed outlier: 3.848A  pdb=" N   LEU D 252 " --> pdb=" O   PRO D 248 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER D 263 " --> pdb=" O   TRP D 259 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ALA D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 26
      removed outlier: 5.365A  pdb=" N   LEU B  22 " --> pdb=" O   GLY B   8 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLN B  59 " --> pdb=" O   GLN B   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 13
    Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 153
      removed outlier: 6.282A  pdb=" N   VAL B  31 " --> pdb=" O   ARG B 197 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   ALA B 199 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLY B  33 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU B 201 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   PHE B  35 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 255
      removed outlier: 3.787A  pdb=" N   ILE B 255 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL B 223 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 254 through 255
      removed outlier: 3.787A  pdb=" N   ILE B 255 " --> pdb=" O   ALA B 227 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26
      removed outlier: 5.978A  pdb=" N   LEU C  22 " --> pdb=" O   GLY C   8 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLN C   7 " --> pdb=" O   GLN C  59 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN C  59 " --> pdb=" O   GLN C   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13
    Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 153
    Processing sheet with id=AA9, first strand: chain 'C' and resid 254 through 258
      removed outlier: 3.659A  pdb=" N   ILE C 255 " --> pdb=" O   ALA C 227 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 37 through 40
      removed outlier: 8.000A  pdb=" N   ARG A  44 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   TRP A  45 " --> pdb=" O   ARG A  65 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 52 through 53
      removed outlier: 3.734A  pdb=" N   GLN A  73 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   THR A  94 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ILE A 147 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL A 177 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   ILE A 199 " --> pdb=" O   ARG A 222 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   THR A 221 " --> pdb=" O   GLU A 244 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   SER A 243 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL A 266 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 56 through 58
      removed outlier: 3.550A  pdb=" N   ASP A 135 " --> pdb=" O   ILE A 111 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   ILE A 162 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   ASP A 187 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU A 164 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ILE A 184 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   MET A 209 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ILE A 186 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   ALA A 229 " --> pdb=" O   TYR A 204 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   VAL A 206 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   MET A 231 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   TYR A 208 " --> pdb=" O   MET A 231 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   THR A 226 " --> pdb=" O   GLY A 250 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   LEU A 252 " --> pdb=" O   THR A 226 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   TYR A 228 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASN A 254 " --> pdb=" O   TYR A 228 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   LEU A 230 " --> pdb=" O   ASN A 254 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   LEU A 288 " --> pdb=" O   GLY A 250 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   LEU A 252 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   ILE A 290 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ASN A 254 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   LYS A 286 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   HIS A 311 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   LEU A 288 " --> pdb=" O   HIS A 311 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   GLN A 332 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 89 through 91
      removed outlier: 6.541A  pdb=" N   VAL A  90 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 215 through 217
      removed outlier: 6.248A  pdb=" N   LEU A 216 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 7.524A  pdb=" N   SER A 322 " --> pdb=" O   ASN A 296 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   ILE A 298 " --> pdb=" O   SER A 322 " (cutoff:3.500A)

    524 hydrogen bonds defined for protein.
    1476 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: 1.76

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3661
        1.33 -     1.45: 2211
        1.45 -     1.57: 5972
        1.57 -     1.69: 6
        1.69 -     1.81: 62
  Bond restraints: 11912
  Sorted by residual:
  bond pdb=" O3A ANP B 402 "
       pdb=" PB  ANP B 402 "
    ideal  model  delta    sigma   weight residual
    1.700  1.529  0.171 2.00e-02 2.50e+03 7.30e+01
  bond pdb=" O3A ANP C 402 "
       pdb=" PB  ANP C 402 "
    ideal  model  delta    sigma   weight residual
    1.700  1.532  0.168 2.00e-02 2.50e+03 7.03e+01
  bond pdb=" N3B ANP C 402 "
       pdb=" PG  ANP C 402 "
    ideal  model  delta    sigma   weight residual
    1.795  1.679  0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" N3B ANP B 402 "
       pdb=" PG  ANP B 402 "
    ideal  model  delta    sigma   weight residual
    1.795  1.680  0.115 2.00e-02 2.50e+03 3.28e+01
  bond pdb=" O5' ANP B 402 "
       pdb=" PA  ANP B 402 "
    ideal  model  delta    sigma   weight residual
    1.655  1.557  0.098 2.00e-02 2.50e+03 2.42e+01
  ... (remaining 11907 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.68: 16012
        4.68 -     9.35: 152
        9.35 -    14.03: 14
       14.03 -    18.70: 5
       18.70 -    23.38: 2
  Bond angle restraints: 16185
  Sorted by residual:
  angle pdb=" PB  ANP C 402 "
        pdb=" N3B ANP C 402 "
        pdb=" PG  ANP C 402 "
      ideal   model   delta    sigma   weight residual
     126.95  103.57   23.38 3.00e+00 1.11e-01 6.07e+01
  angle pdb=" PB  ANP B 402 "
        pdb=" N3B ANP B 402 "
        pdb=" PG  ANP B 402 "
      ideal   model   delta    sigma   weight residual
     126.95  105.67   21.28 3.00e+00 1.11e-01 5.03e+01
  angle pdb=" CG1 VAL B  31 "
        pdb=" CB  VAL B  31 "
        pdb=" CG2 VAL B  31 "
      ideal   model   delta    sigma   weight residual
     110.80   99.06   11.74 2.20e+00 2.07e-01 2.85e+01
  angle pdb=" PA  ANP B 402 "
        pdb=" O3A ANP B 402 "
        pdb=" PB  ANP B 402 "
      ideal   model   delta    sigma   weight residual
     125.41  109.66   15.75 3.00e+00 1.11e-01 2.75e+01
  angle pdb=" PA  ANP C 402 "
        pdb=" O3A ANP C 402 "
        pdb=" PB  ANP C 402 "
      ideal   model   delta    sigma   weight residual
     125.41  110.62   14.79 3.00e+00 1.11e-01 2.43e+01
  ... (remaining 16180 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.39: 6547
       22.39 -    44.77: 436
       44.77 -    67.15: 64
       67.15 -    89.54: 19
       89.54 -   111.92: 2
  Dihedral angle restraints: 7068
    sinusoidal: 2809
      harmonic: 4259
  Sorted by residual:
  dihedral pdb=" CA  LEU D  73 "
           pdb=" C   LEU D  73 "
           pdb=" N   ALA D  74 "
           pdb=" CA  ALA D  74 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.96  -22.04     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  LEU E  73 "
           pdb=" C   LEU E  73 "
           pdb=" N   ALA E  74 "
           pdb=" CA  ALA E  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.56  -21.44     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  SER D 240 "
           pdb=" C   SER D 240 "
           pdb=" N   LEU D 241 "
           pdb=" CA  LEU D 241 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.60   21.40     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 7065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 1620
       0.102 -    0.203: 216
       0.203 -    0.305: 22
       0.305 -    0.407: 6
       0.407 -    0.508: 1
  Chirality restraints: 1865
  Sorted by residual:
  chirality pdb=" CB  VAL A 413 "
            pdb=" CA  VAL A 413 "
            pdb=" CG1 VAL A 413 "
            pdb=" CG2 VAL A 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.12   -0.51 2.00e-01 2.50e+01 6.46e+00
  chirality pdb=" CB  VAL C 187 "
            pdb=" CA  VAL C 187 "
            pdb=" CG1 VAL C 187 "
            pdb=" CG2 VAL C 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.23   -0.40 2.00e-01 2.50e+01 4.03e+00
  chirality pdb=" CB  ILE B 255 "
            pdb=" CA  ILE B 255 "
            pdb=" CG1 ILE B 255 "
            pdb=" CG2 ILE B 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 1862 not shown)

  Planarity restraints: 2060
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 187 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   VAL B 187 "    0.059 2.00e-02 2.50e+03
        pdb=" O   VAL B 187 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 188 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET D  66 "    0.051 5.00e-02 4.00e+02   7.62e-02 9.29e+00
        pdb=" N   PRO D  67 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO D  67 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  67 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  97 "    0.014 2.00e-02 2.50e+03   2.94e-02 8.66e+00
        pdb=" C   GLU A  97 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   GLU A  97 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TRP A  98 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2057 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 31
        2.37 -     3.00: 5864
        3.00 -     3.63: 18585
        3.63 -     4.27: 28575
        4.27 -     4.90: 46732
  Nonbonded interactions: 99787
  Sorted by model distance:
  nonbonded pdb="MG    MG A 501 "
            pdb=" O   HOH A 601 "
     model   vdw
     1.734 2.170
  nonbonded pdb=" OD1 ASP A 359 "
            pdb="MG    MG A 501 "
     model   vdw
     1.944 2.170
  nonbonded pdb="MG    MG B 401 "
            pdb=" O2G ANP B 402 "
     model   vdw
     2.095 2.170
  nonbonded pdb="MG    MG B 401 "
            pdb=" O2B ANP B 402 "
     model   vdw
     2.106 2.170
  nonbonded pdb="MG    MG C 401 "
            pdb=" O2G ANP C 402 "
     model   vdw
     2.107 2.170
  ... (remaining 99782 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 'B'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'D' and (resid 2 through 42 or resid 51 through 132 or resid 136 through  \ 
228 or resid 245 through 274))
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     10.980
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
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      :  0.012   0.171  11912  Z= 0.536
  Angle     :  1.294  23.378  16185  Z= 0.647
  Chirality :  0.073   0.508   1865
  Planarity :  0.008   0.076   2060
  Dihedral  : 15.583 111.922   4352
  Min Nonbonded Distance : 1.734

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.50 %
    Favored  : 89.68 %
  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 are not related in a simple way.
  whole: -5.32 (0.15), residues: 1493
  helix: -4.25 (0.09), residues: 639
  sheet: -3.34 (0.30), residues: 194
  loop : -2.63 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 360 
 TYR   0.026   0.003   TYR E  93 
 PHE   0.022   0.003   PHE A  56 
 TRP   0.040   0.003   TRP A  45 
 HIS   0.010   0.002   HIS A 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.01173 (11912)
  covalent geometry    : angle       1.29443 (16185)
  hydrogen bonds       : bond        0.29050 (  523)
  hydrogen bonds       : angle      10.67804 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   16 MET cc_start: 0.8580 (tmm) cc_final: 0.8304 (tmm)
REVERT: B   61 LYS cc_start: 0.9060 (mtpt) cc_final: 0.8748 (tppt)
REVERT: B  200 ILE cc_start: 0.9798 (mt) cc_final: 0.9536 (tt)
REVERT: C   46 MET cc_start: 0.9251 (mtm) cc_final: 0.9048 (mtm)
REVERT: C   83 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8828 (p)
REVERT: C  295 MET cc_start: 0.8078 (mmm) cc_final: 0.7064 (mmm)
REVERT: A   62 MET cc_start: 0.8065 (mmp) cc_final: 0.7818 (mmm)
REVERT: A  103 THR cc_start: 0.9281 (p) cc_final: 0.9081 (p)
REVERT: A  235 LYS cc_start: 0.9338 (mmtt) cc_final: 0.9002 (tppt)
REVERT: A  334 LYS cc_start: 0.9540 (tttt) cc_final: 0.8928 (ttmm)
REVERT: E   66 MET cc_start: 0.9390 (mmm) cc_final: 0.9083 (mpp)
REVERT: E  138 MET cc_start: 0.8877 (tpt) cc_final: 0.8568 (tpp)
REVERT: E  171 LYS cc_start: 0.9204 (tttt) cc_final: 0.8974 (tmmt)
REVERT: E  213 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9256 (mm)
REVERT: E  255 CYS cc_start: 0.9128 (t) cc_final: 0.8716 (t)
REVERT: D   82 ASP cc_start: 0.8899 (t70) cc_final: 0.8611 (t0)
REVERT: D   83 GLU cc_start: 0.9154 (pt0) cc_final: 0.8734 (pp20)
REVERT: D  138 MET cc_start: 0.8849 (tmm) cc_final: 0.8294 (tmm)
REVERT: D  171 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8941 (ttmm)
REVERT: D  219 ASP cc_start: 0.9182 (m-30) cc_final: 0.8977 (m-30)
  outliers start: 10
  outliers final: 3
  residues processed: 104
  average time/residue: 0.1166
  time to fit residues: 17.2852
Evaluate side-chains
  69 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain D residue  131 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B  97 HIS
B 115 GLN
B 283 HIS
C 207 GLN
C 263 HIS
A  30 GLN
A  53 GLN
A  77 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 ASN
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 176 HIS
A 179 ASN
A 190 ASN
A 193 HIS
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 212 ASN
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 292 ASN
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 341 GLN
A 373 ASN
A 417 HIS
D 225 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.044787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.034383 restraints weight = 74585.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.035577 restraints weight = 38046.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.036360 restraints weight = 24778.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.036853 restraints weight = 18570.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.037246 restraints weight = 15311.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11912  Z= 0.129
  Angle     :  0.629   9.890  16185  Z= 0.319
  Chirality :  0.043   0.175   1865
  Planarity :  0.005   0.068   2060
  Dihedral  :  9.568 135.009   1709
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 13.60 %
    Favored  : 84.28 %
  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 are not related in a simple way.
  whole: -3.00 (0.19), residues: 1493
  helix: -1.52 (0.17), residues: 663
  sheet: -3.04 (0.31), residues: 199
  loop : -1.96 (0.24), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 269 
 TYR   0.011   0.001   TYR E 221 
 PHE   0.009   0.001   PHE E 157 
 TRP   0.012   0.001   TRP D 253 
 HIS   0.010   0.001   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (11912)
  covalent geometry    : angle       0.62908 (16185)
  hydrogen bonds       : bond        0.04092 (  523)
  hydrogen bonds       : angle       5.45368 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8804 (tppt)
REVERT: C   16 MET cc_start: 0.8458 (tmm) cc_final: 0.8248 (tmm)
REVERT: C   37 HIS cc_start: 0.8107 (m-70) cc_final: 0.7387 (m90)
REVERT: C  112 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9396 (mm)
REVERT: C  268 LEU cc_start: 0.9601 (mt) cc_final: 0.9378 (mt)
REVERT: C  295 MET cc_start: 0.8143 (mmm) cc_final: 0.7236 (mmm)
REVERT: A  231 MET cc_start: 0.9185 (mtp) cc_final: 0.8925 (mtp)
REVERT: A  235 LYS cc_start: 0.9285 (mmtt) cc_final: 0.9000 (tppt)
REVERT: A  334 LYS cc_start: 0.9485 (tttt) cc_final: 0.9039 (ttmm)
REVERT: E  143 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8947 (m-10)
REVERT: E  212 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8871 (mp)
REVERT: E  213 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9232 (mm)
REVERT: E  255 CYS cc_start: 0.8813 (t) cc_final: 0.8357 (t)
REVERT: D   82 ASP cc_start: 0.8799 (t70) cc_final: 0.8505 (t0)
REVERT: D   83 GLU cc_start: 0.8996 (pt0) cc_final: 0.8576 (pp20)
REVERT: D  114 LEU cc_start: 0.8943 (tt) cc_final: 0.8531 (mp)
REVERT: D  138 MET cc_start: 0.8842 (tmm) cc_final: 0.8380 (tmm)
REVERT: D  170 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6962 (pm20)
REVERT: D  255 CYS cc_start: 0.9227 (t) cc_final: 0.8775 (t)
  outliers start: 26
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0952
  time to fit residues: 15.9210
Evaluate side-chains
  82 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  269 ARG
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  170 GLU
Chi-restraints excluded: chain D residue  208 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 58 optimal weight:    9.9990
   chunk 138 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 114 optimal weight:    7.9990
   chunk 123 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 141 optimal weight:    7.9990
   chunk 146 optimal weight:    0.8980
   chunk 144 optimal weight:    8.9990
   chunk 112 optimal weight:    2.9990
   chunk 147 optimal weight:    0.5980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 214 GLN
C 214 GLN
A  63 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 373 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.044162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.033716 restraints weight = 77130.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.034861 restraints weight = 40169.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.035626 restraints weight = 26515.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.036137 restraints weight = 20028.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.036502 restraints weight = 16546.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11912  Z= 0.189
  Angle     :  0.638  10.692  16185  Z= 0.317
  Chirality :  0.042   0.161   1865
  Planarity :  0.004   0.040   2060
  Dihedral  :  7.924 132.714   1708
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.91 %
    Favored  : 82.80 %
  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 are not related in a simple way.
  whole: -1.65 (0.22), residues: 1493
  helix:  0.07 (0.20), residues: 663
  sheet: -2.81 (0.33), residues: 203
  loop : -1.67 (0.25), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 269 
 TYR   0.008   0.001   TYR E  93 
 PHE   0.014   0.001   PHE E 157 
 TRP   0.008   0.001   TRP D  20 
 HIS   0.002   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (11912)
  covalent geometry    : angle       0.63825 (16185)
  hydrogen bonds       : bond        0.03607 (  523)
  hydrogen bonds       : angle       4.82914 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 73
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8800 (tppt)
REVERT: C   37 HIS cc_start: 0.8160 (m-70) cc_final: 0.7680 (m90)
REVERT: C  112 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9396 (mm)
REVERT: C  268 LEU cc_start: 0.9619 (mt) cc_final: 0.9404 (mt)
REVERT: C  295 MET cc_start: 0.8410 (mmm) cc_final: 0.7243 (mmm)
REVERT: A  235 LYS cc_start: 0.9287 (mmtt) cc_final: 0.9079 (tppt)
REVERT: A  334 LYS cc_start: 0.9514 (tttt) cc_final: 0.9181 (tttp)
REVERT: E  212 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8884 (mp)
REVERT: E  255 CYS cc_start: 0.8732 (t) cc_final: 0.8359 (t)
REVERT: D   82 ASP cc_start: 0.8776 (t70) cc_final: 0.8479 (t0)
REVERT: D   83 GLU cc_start: 0.8959 (pt0) cc_final: 0.8552 (pp20)
REVERT: D  114 LEU cc_start: 0.8972 (tt) cc_final: 0.8556 (mp)
REVERT: D  138 MET cc_start: 0.8868 (tmm) cc_final: 0.8413 (tmm)
REVERT: D  170 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7107 (pm20)
REVERT: D  201 GLU cc_start: 0.8239 (mp0) cc_final: 0.7970 (mp0)
REVERT: D  255 CYS cc_start: 0.9235 (t) cc_final: 0.8849 (t)
  outliers start: 28
  outliers final: 19
  residues processed: 99
  average time/residue: 0.0859
  time to fit residues: 13.3815
Evaluate side-chains
  84 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  269 ARG
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  225 ILE
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  219 ASP
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  170 GLU
Chi-restraints excluded: chain D residue  247 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 131 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 138 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 194 HIS
B 283 HIS
C 283 HIS
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.043539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.033354 restraints weight = 77838.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.034498 restraints weight = 41398.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.035247 restraints weight = 27573.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.035719 restraints weight = 20968.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.036071 restraints weight = 17468.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  11912  Z= 0.276
  Angle     :  0.703  12.181  16185  Z= 0.345
  Chirality :  0.044   0.151   1865
  Planarity :  0.004   0.036   2060
  Dihedral  :  7.548 131.477   1706
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.22 %
    Favored  : 80.59 %
  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 are not related in a simple way.
  whole: -1.13 (0.22), residues: 1493
  helix:  0.68 (0.21), residues: 663
  sheet: -2.46 (0.36), residues: 191
  loop : -1.71 (0.25), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 269 
 TYR   0.009   0.001   TYR E  93 
 PHE   0.017   0.002   PHE E 157 
 TRP   0.011   0.001   TRP A  45 
 HIS   0.003   0.001   HIS C 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 (11912)
  covalent geometry    : angle       0.70338 (16185)
  hydrogen bonds       : bond        0.03518 (  523)
  hydrogen bonds       : angle       4.71918 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 65
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 HIS cc_start: 0.8007 (m-70) cc_final: 0.7356 (m-70)
REVERT: C  112 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9426 (mm)
REVERT: C  133 MET cc_start: 0.9091 (mtm) cc_final: 0.8783 (ptp)
REVERT: C  268 LEU cc_start: 0.9644 (mt) cc_final: 0.9425 (mt)
REVERT: C  295 MET cc_start: 0.8436 (mmm) cc_final: 0.7242 (mmm)
REVERT: A  231 MET cc_start: 0.9296 (mtp) cc_final: 0.9032 (mtp)
REVERT: A  334 LYS cc_start: 0.9539 (tttt) cc_final: 0.9231 (tttp)
REVERT: E   35 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8839 (tt)
REVERT: E  212 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8924 (mp)
REVERT: E  252 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9062 (tp)
REVERT: E  255 CYS cc_start: 0.8770 (t) cc_final: 0.8412 (t)
REVERT: D   11 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8007 (mm-30)
REVERT: D   82 ASP cc_start: 0.8875 (t70) cc_final: 0.8565 (t0)
REVERT: D   83 GLU cc_start: 0.8938 (pt0) cc_final: 0.8646 (pp20)
REVERT: D  138 MET cc_start: 0.8891 (tmm) cc_final: 0.8348 (tmm)
REVERT: D  201 GLU cc_start: 0.8395 (mp0) cc_final: 0.8091 (mp0)
REVERT: D  255 CYS cc_start: 0.9241 (t) cc_final: 0.8904 (t)
  outliers start: 39
  outliers final: 20
  residues processed: 99
  average time/residue: 0.0819
  time to fit residues: 12.7424
Evaluate side-chains
  81 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  269 ARG
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  247 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 143 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 91 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.045873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.035615 restraints weight = 76424.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.036814 restraints weight = 39656.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.037625 restraints weight = 25982.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.038165 restraints weight = 19526.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.038499 restraints weight = 16016.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11912  Z= 0.114
  Angle     :  0.583   9.750  16185  Z= 0.286
  Chirality :  0.041   0.161   1865
  Planarity :  0.003   0.041   2060
  Dihedral  :  7.400 132.200   1704
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.44 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.23), residues: 1493
  helix:  0.95 (0.21), residues: 668
  sheet: -2.34 (0.35), residues: 202
  loop : -1.48 (0.26), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 269 
 TYR   0.007   0.001   TYR E 221 
 PHE   0.010   0.001   PHE E  64 
 TRP   0.008   0.001   TRP C 236 
 HIS   0.002   0.000   HIS B  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (11912)
  covalent geometry    : angle       0.58349 (16185)
  hydrogen bonds       : bond        0.03105 (  523)
  hydrogen bonds       : angle       4.34267 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 HIS cc_start: 0.8166 (m-70) cc_final: 0.7456 (m-70)
REVERT: C  112 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9354 (mm)
REVERT: C  133 MET cc_start: 0.9097 (mtm) cc_final: 0.8682 (ptp)
REVERT: C  268 LEU cc_start: 0.9603 (mt) cc_final: 0.9384 (mt)
REVERT: C  295 MET cc_start: 0.8393 (mmm) cc_final: 0.7160 (mmm)
REVERT: A  334 LYS cc_start: 0.9489 (tttt) cc_final: 0.9181 (tttp)
REVERT: E  143 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8952 (m-10)
REVERT: E  212 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8908 (mp)
REVERT: E  252 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9018 (tp)
REVERT: E  255 CYS cc_start: 0.8751 (t) cc_final: 0.8398 (t)
REVERT: D   11 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8046 (tm-30)
REVERT: D   82 ASP cc_start: 0.8756 (t70) cc_final: 0.8519 (t0)
REVERT: D   83 GLU cc_start: 0.8925 (pt0) cc_final: 0.8583 (pp20)
REVERT: D  114 LEU cc_start: 0.8881 (tt) cc_final: 0.8522 (mt)
REVERT: D  138 MET cc_start: 0.8888 (tmm) cc_final: 0.8525 (tmm)
REVERT: D  201 GLU cc_start: 0.8346 (mp0) cc_final: 0.8035 (mp0)
REVERT: D  255 CYS cc_start: 0.9237 (t) cc_final: 0.8890 (t)
  outliers start: 30
  outliers final: 15
  residues processed: 94
  average time/residue: 0.0743
  time to fit residues: 11.7384
Evaluate side-chains
  82 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  139 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 88 optimal weight:    4.9990
   chunk 67 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 49 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 144 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.043676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.033441 restraints weight = 80001.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.034570 restraints weight = 42715.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.035331 restraints weight = 28647.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.035769 restraints weight = 21818.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.036130 restraints weight = 18334.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.055  11912  Z= 0.367
  Angle     :  0.776  12.516  16185  Z= 0.376
  Chirality :  0.045   0.150   1865
  Planarity :  0.004   0.035   2060
  Dihedral  :  7.447 131.427   1704
  Min Nonbonded Distance : 1.837

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.02 %
    Favored  : 78.38 %
  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 are not related in a simple way.
  whole: -0.70 (0.23), residues: 1493
  helix:  1.07 (0.21), residues: 670
  sheet: -2.24 (0.35), residues: 214
  loop : -1.51 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 126 
 TYR   0.010   0.002   TYR D 221 
 PHE   0.018   0.002   PHE E 157 
 TRP   0.012   0.001   TRP A  45 
 HIS   0.004   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00772 (11912)
  covalent geometry    : angle       0.77632 (16185)
  hydrogen bonds       : bond        0.03567 (  523)
  hydrogen bonds       : angle       4.68426 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 63
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  269 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8515 (tpp-160)
REVERT: B  295 MET cc_start: 0.8648 (mmm) cc_final: 0.8248 (mtp)
REVERT: C   46 MET cc_start: 0.9349 (ptp) cc_final: 0.8956 (ptp)
REVERT: C  112 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9449 (mm)
REVERT: C  133 MET cc_start: 0.9125 (mtm) cc_final: 0.8740 (ptp)
REVERT: C  268 LEU cc_start: 0.9628 (mt) cc_final: 0.9385 (mt)
REVERT: A  334 LYS cc_start: 0.9561 (tttt) cc_final: 0.9113 (ttmm)
REVERT: E   35 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8844 (tt)
REVERT: E  143 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8922 (m-10)
REVERT: E  212 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8992 (mp)
REVERT: E  252 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9098 (tp)
REVERT: E  255 CYS cc_start: 0.8788 (t) cc_final: 0.8441 (t)
REVERT: D   11 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8036 (mm-30)
REVERT: D   82 ASP cc_start: 0.8953 (t70) cc_final: 0.8678 (t0)
REVERT: D   83 GLU cc_start: 0.9015 (pt0) cc_final: 0.8695 (pp20)
REVERT: D  138 MET cc_start: 0.8959 (tmm) cc_final: 0.8569 (tmm)
REVERT: D  201 GLU cc_start: 0.8552 (mp0) cc_final: 0.8195 (mp0)
REVERT: D  255 CYS cc_start: 0.9231 (t) cc_final: 0.8887 (t)
  outliers start: 44
  outliers final: 32
  residues processed: 101
  average time/residue: 0.0754
  time to fit residues: 12.3100
Evaluate side-chains
  96 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 58
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain B residue  269 ARG
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain E residue   35 ILE
Chi-restraints excluded: chain E residue   55 ILE
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  110 LEU
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  177 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  260 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 125 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 141 optimal weight:    3.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.045189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.034946 restraints weight = 77238.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.036139 restraints weight = 40044.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.036934 restraints weight = 26269.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.037434 restraints weight = 19780.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.037793 restraints weight = 16372.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11912  Z= 0.148
  Angle     :  0.610  10.587  16185  Z= 0.297
  Chirality :  0.042   0.156   1865
  Planarity :  0.003   0.039   2060
  Dihedral  :  7.339 131.623   1704
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.67 %
    Favored  : 78.46 %
  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 are not related in a simple way.
  whole: -0.41 (0.23), residues: 1493
  helix:  1.31 (0.21), residues: 670
  sheet: -2.10 (0.35), residues: 209
  loop : -1.36 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 269 
 TYR   0.016   0.001   TYR D 221 
 PHE   0.010   0.001   PHE E 157 
 TRP   0.008   0.001   TRP B 236 
 HIS   0.003   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11912)
  covalent geometry    : angle       0.61002 (16185)
  hydrogen bonds       : bond        0.03110 (  523)
  hydrogen bonds       : angle       4.31400 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 66
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  295 MET cc_start: 0.8564 (mmm) cc_final: 0.8314 (mtp)
REVERT: C   37 HIS cc_start: 0.8356 (m90) cc_final: 0.7643 (m90)
REVERT: C   83 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.8988 (t)
REVERT: C  112 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9369 (mm)
REVERT: C  133 MET cc_start: 0.9104 (mtm) cc_final: 0.8662 (ptp)
REVERT: C  268 LEU cc_start: 0.9610 (mt) cc_final: 0.9395 (mt)
REVERT: A   62 MET cc_start: 0.8061 (mmp) cc_final: 0.7853 (mmm)
REVERT: A  334 LYS cc_start: 0.9515 (tttt) cc_final: 0.9182 (tttp)
REVERT: E  138 MET cc_start: 0.8834 (tpt) cc_final: 0.8550 (tpp)
REVERT: E  143 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8876 (m-10)
REVERT: E  212 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8893 (mp)
REVERT: E  252 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9037 (tp)
REVERT: E  255 CYS cc_start: 0.8760 (t) cc_final: 0.8414 (t)
REVERT: D   11 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: D   81 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8203 (mm-30)
REVERT: D   82 ASP cc_start: 0.8860 (t70) cc_final: 0.8559 (t0)
REVERT: D   83 GLU cc_start: 0.8918 (pt0) cc_final: 0.8578 (pp20)
REVERT: D  114 LEU cc_start: 0.8902 (tt) cc_final: 0.8527 (mt)
REVERT: D  138 MET cc_start: 0.8925 (tmm) cc_final: 0.8553 (tmm)
REVERT: D  201 GLU cc_start: 0.8505 (mp0) cc_final: 0.8133 (mp0)
REVERT: D  255 CYS cc_start: 0.9230 (t) cc_final: 0.8898 (t)
  outliers start: 35
  outliers final: 23
  residues processed: 97
  average time/residue: 0.0721
  time to fit residues: 11.7015
Evaluate side-chains
  91 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 63
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  213 LEU
Chi-restraints excluded: chain E residue  219 ASP
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain E residue  260 ILE
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  177 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 126 optimal weight:    0.9990
   chunk 29 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 133 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0470
   chunk 90 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0670
   chunk 130 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.0222

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

Flipped N/Q/H residues before XYZ refinement:
B  82 ASN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.047142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.036817 restraints weight = 75709.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.038015 restraints weight = 38917.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.038792 restraints weight = 25451.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.039311 restraints weight = 19209.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.039621 restraints weight = 15836.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11912  Z= 0.120
  Angle     :  0.595  10.910  16185  Z= 0.289
  Chirality :  0.041   0.156   1865
  Planarity :  0.003   0.040   2060
  Dihedral  :  7.213 131.798   1704
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.92 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.23), residues: 1493
  helix:  1.41 (0.21), residues: 670
  sheet: -2.02 (0.35), residues: 209
  loop : -1.27 (0.27), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 292 
 TYR   0.013   0.001   TYR D 221 
 PHE   0.010   0.001   PHE E 157 
 TRP   0.008   0.001   TRP C 236 
 HIS   0.006   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11912)
  covalent geometry    : angle       0.59509 (16185)
  hydrogen bonds       : bond        0.02979 (  523)
  hydrogen bonds       : angle       4.16249 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 64
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  295 MET cc_start: 0.8491 (mmm) cc_final: 0.8251 (mtp)
REVERT: C   83 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.8958 (t)
REVERT: C  112 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9346 (mm)
REVERT: C  133 MET cc_start: 0.9107 (mtm) cc_final: 0.8740 (ptp)
REVERT: C  268 LEU cc_start: 0.9609 (mt) cc_final: 0.9405 (mt)
REVERT: A   62 MET cc_start: 0.8023 (mmp) cc_final: 0.7810 (mmm)
REVERT: A  334 LYS cc_start: 0.9494 (tttt) cc_final: 0.9169 (tttp)
REVERT: E  138 MET cc_start: 0.8846 (tpt) cc_final: 0.8563 (tpp)
REVERT: E  143 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8880 (m-10)
REVERT: E  212 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8847 (mp)
REVERT: E  252 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9051 (tp)
REVERT: E  255 CYS cc_start: 0.8646 (t) cc_final: 0.8324 (t)
REVERT: D   11 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8015 (mm-30)
REVERT: D   82 ASP cc_start: 0.8824 (t70) cc_final: 0.8530 (t0)
REVERT: D   83 GLU cc_start: 0.8889 (pt0) cc_final: 0.8564 (pp20)
REVERT: D  114 LEU cc_start: 0.8816 (tt) cc_final: 0.8456 (mt)
REVERT: D  138 MET cc_start: 0.8928 (tmm) cc_final: 0.8540 (tmm)
REVERT: D  201 GLU cc_start: 0.8459 (mp0) cc_final: 0.8061 (mp0)
REVERT: D  255 CYS cc_start: 0.9221 (t) cc_final: 0.8893 (t)
  outliers start: 35
  outliers final: 26
  residues processed: 93
  average time/residue: 0.0797
  time to fit residues: 12.2202
Evaluate side-chains
  93 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 62
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   82 ASN
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain E residue   55 ILE
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  212 LEU
Chi-restraints excluded: chain E residue  219 ASP
Chi-restraints excluded: chain E residue  252 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  177 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 119 optimal weight:    0.0010
   chunk 93 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 89 optimal weight:    8.9990
   chunk 126 optimal weight:    1.9990
   chunk 112 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 131 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   chunk 140 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.0990

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

Flipped N/Q/H residues before XYZ refinement:
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.045511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.035354 restraints weight = 74008.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.036519 restraints weight = 39111.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.037250 restraints weight = 25895.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.037777 restraints weight = 19735.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.038140 restraints weight = 16228.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11912  Z= 0.121
  Angle     :  0.597  11.183  16185  Z= 0.290
  Chirality :  0.042   0.178   1865
  Planarity :  0.003   0.041   2060
  Dihedral  :  7.168 131.491   1704
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 19.25 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.23), residues: 1493
  helix:  1.41 (0.21), residues: 682
  sheet: -1.95 (0.35), residues: 209
  loop : -1.44 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 269 
 TYR   0.012   0.001   TYR D 221 
 PHE   0.010   0.001   PHE E 157 
 TRP   0.007   0.001   TRP A  98 
 HIS   0.017   0.001   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (11912)
  covalent geometry    : angle       0.59739 (16185)
  hydrogen bonds       : bond        0.02942 (  523)
  hydrogen bonds       : angle       4.15441 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 64
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  295 MET cc_start: 0.8429 (mmm) cc_final: 0.8193 (mtp)
REVERT: C   83 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.8974 (t)
REVERT: C  112 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9357 (mm)
REVERT: C  133 MET cc_start: 0.9090 (mtm) cc_final: 0.8697 (ptp)
REVERT: C  268 LEU cc_start: 0.9582 (mt) cc_final: 0.9377 (mt)
REVERT: A   62 MET cc_start: 0.7981 (mmp) cc_final: 0.7771 (mmm)
REVERT: A  209 MET cc_start: 0.7175 (mmt) cc_final: 0.6564 (mmm)
REVERT: A  279 MET cc_start: 0.8035 (tmm) cc_final: 0.7689 (tmm)
REVERT: A  334 LYS cc_start: 0.9486 (tttt) cc_final: 0.9053 (ttmm)
REVERT: E  138 MET cc_start: 0.8819 (tpt) cc_final: 0.8543 (tpp)
REVERT: E  143 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8898 (m-10)
REVERT: E  255 CYS cc_start: 0.8672 (t) cc_final: 0.8358 (t)
REVERT: D   11 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8027 (mm-30)
REVERT: D   82 ASP cc_start: 0.8816 (t70) cc_final: 0.8588 (t0)
REVERT: D   83 GLU cc_start: 0.8912 (pt0) cc_final: 0.8581 (pp20)
REVERT: D  114 LEU cc_start: 0.8814 (tt) cc_final: 0.8466 (mt)
REVERT: D  138 MET cc_start: 0.8927 (tmm) cc_final: 0.8534 (tmm)
REVERT: D  201 GLU cc_start: 0.8426 (mp0) cc_final: 0.8032 (mp0)
REVERT: D  255 CYS cc_start: 0.9208 (t) cc_final: 0.8897 (t)
  outliers start: 32
  outliers final: 24
  residues processed: 91
  average time/residue: 0.0775
  time to fit residues: 11.5915
Evaluate side-chains
  89 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain E residue   55 ILE
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  177 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 146 optimal weight:    0.0370
   chunk 134 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 127 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   overall best weight:    1.8064

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

Flipped N/Q/H residues before XYZ refinement:
B  82 ASN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.045501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.035303 restraints weight = 76917.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.036475 restraints weight = 40205.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.037224 restraints weight = 26414.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.037759 restraints weight = 20095.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.038067 restraints weight = 16565.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11912  Z= 0.162
  Angle     :  0.620  11.147  16185  Z= 0.300
  Chirality :  0.042   0.176   1865
  Planarity :  0.003   0.039   2060
  Dihedral  :  7.130 130.652   1704
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.33 %
    Favored  : 78.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.23), residues: 1493
  helix:  1.46 (0.21), residues: 681
  sheet: -1.91 (0.35), residues: 209
  loop : -1.39 (0.27), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 269 
 TYR   0.016   0.001   TYR C 291 
 PHE   0.012   0.001   PHE E 157 
 TRP   0.011   0.001   TRP E 211 
 HIS   0.004   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11912)
  covalent geometry    : angle       0.62046 (16185)
  hydrogen bonds       : bond        0.02987 (  523)
  hydrogen bonds       : angle       4.18889 ( 1476)

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

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

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2986 Ramachandran restraints generated.
    1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 63
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   83 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.8985 (t)
REVERT: C  112 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9359 (mm)
REVERT: C  133 MET cc_start: 0.9167 (mtm) cc_final: 0.8717 (ptp)
REVERT: C  268 LEU cc_start: 0.9590 (mt) cc_final: 0.9387 (mt)
REVERT: A   62 MET cc_start: 0.7947 (mmp) cc_final: 0.7711 (mmm)
REVERT: A  334 LYS cc_start: 0.9496 (tttt) cc_final: 0.9165 (tttp)
REVERT: E  138 MET cc_start: 0.8813 (tpt) cc_final: 0.8500 (tpp)
REVERT: E  143 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8913 (m-10)
REVERT: E  255 CYS cc_start: 0.8674 (t) cc_final: 0.8362 (t)
REVERT: D   11 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: D   82 ASP cc_start: 0.8871 (t70) cc_final: 0.8581 (t0)
REVERT: D   83 GLU cc_start: 0.8991 (pt0) cc_final: 0.8604 (pp20)
REVERT: D  114 LEU cc_start: 0.8782 (tt) cc_final: 0.8490 (mt)
REVERT: D  138 MET cc_start: 0.8968 (tmm) cc_final: 0.8568 (tmm)
REVERT: D  201 GLU cc_start: 0.8495 (mp0) cc_final: 0.8086 (mp0)
REVERT: D  255 CYS cc_start: 0.9231 (t) cc_final: 0.8912 (t)
  outliers start: 31
  outliers final: 25
  residues processed: 88
  average time/residue: 0.0822
  time to fit residues: 11.9370
Evaluate side-chains
  90 residues out of total 1221 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   82 ASN
Chi-restraints excluded: chain B residue  112 LEU
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  255 ILE
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain E residue   55 ILE
Chi-restraints excluded: chain E residue   64 PHE
Chi-restraints excluded: chain E residue  143 PHE
Chi-restraints excluded: chain E residue  168 VAL
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain D residue   63 THR
Chi-restraints excluded: chain D residue  131 VAL
Chi-restraints excluded: chain D residue  139 LEU
Chi-restraints excluded: chain D residue  177 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 128 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 46 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:   10.0000
   chunk 126 optimal weight:    0.7980
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  82 ASN
** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.045231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.035147 restraints weight = 75196.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.036315 restraints weight = 39579.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.037094 restraints weight = 26089.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.037580 restraints weight = 19601.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.037966 restraints weight = 16191.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11912  Z= 0.143
  Angle     :  0.607  11.150  16185  Z= 0.294
  Chirality :  0.042   0.174   1865
  Planarity :  0.003   0.040   2060
  Dihedral  :  7.112 130.371   1704
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.74 %
    Favored  : 77.97 %
  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 are not related in a simple way.
  whole: -0.20 (0.23), residues: 1493
  helix:  1.52 (0.21), residues: 683
  sheet: -1.92 (0.35), residues: 209
  loop : -1.40 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 145 
 TYR   0.015   0.001   TYR C 291 
 PHE   0.011   0.001   PHE E 157 
 TRP   0.009   0.001   TRP E 211 
 HIS   0.005   0.001   HIS C  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (11912)
  covalent geometry    : angle       0.60679 (16185)
  hydrogen bonds       : bond        0.02974 (  523)
  hydrogen bonds       : angle       4.13360 ( 1476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1675.52 seconds
wall clock time: 29 minutes 57.30 seconds (1797.30 seconds total)