Starting phenix.real_space_refine
on Wed Feb 12 03:01:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cye_30498/02_2025/7cye_30498_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cye_30498/02_2025/7cye_30498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cye_30498/02_2025/7cye_30498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cye_30498/02_2025/7cye_30498.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cye_30498/02_2025/7cye_30498_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cye_30498/02_2025/7cye_30498_neut.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    4797      2.51       5
     N    1146      2.21       5
     O    1281      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7263
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2421
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 17, 'TRANS': 308}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2421
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 17, 'TRANS': 308}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2421
          Classifications: {'peptide': 326}
          Link IDs: {'PTRANS': 17, 'TRANS': 308}
          Chain breaks: 1
  Time building chain proxies: 4.42, per 1000 atoms: 0.61
  Number of scatterers: 7263
  At special positions: 0
  Unit cell: (96.235, 100.287, 69.897, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    1281      8.00
     N    1146      7.00
     C    4797      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.81
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1764

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 0 sheets defined
      62.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 15
      removed outlier: 3.977A  pdb=" N   THR A   9 " --> pdb=" O   SER A   5 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP A  10 " --> pdb=" O   ASN A   6 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY A  13 " --> pdb=" O   THR A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 31
      removed outlier: 3.844A  pdb=" N   LEU A  23 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL A  28 " --> pdb=" O   ILE A  24 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ILE A  29 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 3.541A  pdb=" N   THR A  44 " --> pdb=" O   ALA A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   ILE A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG A  63 " --> pdb=" O   GLY A  59 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN A  64 " --> pdb=" O   MET A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 92
      removed outlier: 3.522A  pdb=" N   SER A  77 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU A  80 " --> pdb=" O   PHE A  76 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL A  85 " --> pdb=" O   GLY A  81 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   PHE A  86 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 104
    Processing helix  chain 'A' and resid 120 through 126
      removed outlier: 3.815A  pdb=" N   GLU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 140
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 3.549A  pdb=" N   VAL A 149 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A 154 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
      removed outlier: 4.174A  pdb=" N   GLU A 217 " --> pdb=" O   PRO A 213 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 236
      removed outlier: 3.503A  pdb=" N   LEU A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLY A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 265
      removed outlier: 3.752A  pdb=" N   SER A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE A 257 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY A 263 " --> pdb=" O   MET A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 277
      removed outlier: 3.576A  pdb=" N   GLY A 271 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG A 274 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LYS A 275 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 297
      Proline residue:  A 288  - end of helix
      removed outlier: 4.382A  pdb=" N   GLY A 292 " --> pdb=" O   PRO A 288 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE A 293 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 294 " --> pdb=" O   VAL A 290 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA A 295 " --> pdb=" O   HIS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 302
      removed outlier: 3.849A  pdb=" N   ILE A 301 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 302 " --> pdb=" O   GLY A 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 302'
    Processing helix  chain 'A' and resid 309 through 318
      removed outlier: 3.717A  pdb=" N   VAL A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL A 315 " --> pdb=" O   GLY A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 359
    Processing helix  chain 'A' and resid 360 through 371
      removed outlier: 3.663A  pdb=" N   LEU A 371 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 15
      removed outlier: 3.976A  pdb=" N   THR B   9 " --> pdb=" O   SER B   5 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP B  10 " --> pdb=" O   ASN B   6 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY B  13 " --> pdb=" O   THR B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 31
      removed outlier: 3.844A  pdb=" N   LEU B  23 " --> pdb=" O   THR B  19 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL B  28 " --> pdb=" O   ILE B  24 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE B  29 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 45
      removed outlier: 3.542A  pdb=" N   THR B  44 " --> pdb=" O   ALA B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   ILE B  62 " --> pdb=" O   GLY B  58 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG B  63 " --> pdb=" O   GLY B  59 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ASN B  64 " --> pdb=" O   MET B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 92
      removed outlier: 3.522A  pdb=" N   SER B  77 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU B  80 " --> pdb=" O   PHE B  76 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL B  85 " --> pdb=" O   GLY B  81 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   PHE B  86 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 104
    Processing helix  chain 'B' and resid 120 through 126
      removed outlier: 3.815A  pdb=" N   GLU B 126 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 140
    Processing helix  chain 'B' and resid 144 through 161
      removed outlier: 3.549A  pdb=" N   VAL B 149 " --> pdb=" O   ILE B 145 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR B 150 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA B 151 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL B 154 " --> pdb=" O   THR B 150 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 220
      removed outlier: 4.173A  pdb=" N   GLU B 217 " --> pdb=" O   PRO B 213 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER B 218 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 236
      removed outlier: 3.503A  pdb=" N   LEU B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLY B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 265
      removed outlier: 3.752A  pdb=" N   SER B 256 " --> pdb=" O   ARG B 252 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE B 257 " --> pdb=" O   GLY B 253 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY B 263 " --> pdb=" O   MET B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 277
      removed outlier: 3.575A  pdb=" N   GLY B 271 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG B 274 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   LYS B 275 " --> pdb=" O   GLY B 271 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   VAL B 276 " --> pdb=" O   GLU B 272 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 297
      Proline residue:  B 288  - end of helix
      removed outlier: 4.382A  pdb=" N   GLY B 292 " --> pdb=" O   PRO B 288 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE B 293 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 294 " --> pdb=" O   VAL B 290 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 295 " --> pdb=" O   HIS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 302
      removed outlier: 3.846A  pdb=" N   ILE B 301 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 302 " --> pdb=" O   GLY B 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 302'
    Processing helix  chain 'B' and resid 309 through 318
      removed outlier: 3.717A  pdb=" N   VAL B 314 " --> pdb=" O   LEU B 310 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL B 315 " --> pdb=" O   GLY B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 359
    Processing helix  chain 'B' and resid 360 through 371
      removed outlier: 3.663A  pdb=" N   LEU B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 15
      removed outlier: 3.975A  pdb=" N   THR C   9 " --> pdb=" O   SER C   5 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP C  10 " --> pdb=" O   ASN C   6 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY C  13 " --> pdb=" O   THR C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 19 through 31
      removed outlier: 3.844A  pdb=" N   LEU C  23 " --> pdb=" O   THR C  19 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   VAL C  28 " --> pdb=" O   ILE C  24 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ILE C  29 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 45
      removed outlier: 3.541A  pdb=" N   THR C  44 " --> pdb=" O   ALA C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 64
      removed outlier: 3.558A  pdb=" N   ILE C  62 " --> pdb=" O   GLY C  58 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ARG C  63 " --> pdb=" O   GLY C  59 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN C  64 " --> pdb=" O   MET C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 92
      removed outlier: 3.522A  pdb=" N   SER C  77 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE C  79 " --> pdb=" O   ALA C  75 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LEU C  80 " --> pdb=" O   PHE C  76 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE C  84 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL C  85 " --> pdb=" O   GLY C  81 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   PHE C  86 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 100 through 104
    Processing helix  chain 'C' and resid 120 through 126
      removed outlier: 3.815A  pdb=" N   GLU C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 140
    Processing helix  chain 'C' and resid 144 through 161
      removed outlier: 3.550A  pdb=" N   VAL C 149 " --> pdb=" O   ILE C 145 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR C 150 " --> pdb=" O   PRO C 146 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ALA C 151 " --> pdb=" O   ALA C 147 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL C 154 " --> pdb=" O   THR C 150 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU C 159 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 220
      removed outlier: 4.174A  pdb=" N   GLU C 217 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   SER C 218 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 236
      removed outlier: 3.503A  pdb=" N   LEU C 228 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLY C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 265
      removed outlier: 3.752A  pdb=" N   SER C 256 " --> pdb=" O   ARG C 252 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE C 257 " --> pdb=" O   GLY C 253 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLY C 263 " --> pdb=" O   MET C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 277
      removed outlier: 3.576A  pdb=" N   GLY C 271 " --> pdb=" O   TRP C 267 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ARG C 274 " --> pdb=" O   ILE C 270 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   LYS C 275 " --> pdb=" O   GLY C 271 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   VAL C 276 " --> pdb=" O   GLU C 272 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA C 277 " --> pdb=" O   LEU C 273 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 279 through 297
      Proline residue:  C 288  - end of helix
      removed outlier: 4.382A  pdb=" N   GLY C 292 " --> pdb=" O   PRO C 288 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   PHE C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE C 294 " --> pdb=" O   VAL C 290 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA C 295 " --> pdb=" O   HIS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 301
      removed outlier: 3.831A  pdb=" N   ILE C 301 " --> pdb=" O   LEU C 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 298 through 301'
    Processing helix  chain 'C' and resid 309 through 318
      removed outlier: 3.717A  pdb=" N   VAL C 314 " --> pdb=" O   LEU C 310 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL C 315 " --> pdb=" O   GLY C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 359
    Processing helix  chain 'C' and resid 360 through 371
      removed outlier: 3.662A  pdb=" N   LEU C 371 " --> pdb=" O   LEU C 367 " (cutoff:3.500A)

    267 hydrogen bonds defined for protein.
    756 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: 1.69

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2089
        1.34 -     1.45: 1256
        1.45 -     1.57: 3996
        1.57 -     1.69: 0
        1.69 -     1.81: 75
  Bond restraints: 7416
  Sorted by residual:
  bond pdb=" N   ILE B 301 "
       pdb=" CA  ILE B 301 "
    ideal  model  delta    sigma   weight residual
    1.460  1.493 -0.033 1.09e-02 8.42e+03 9.31e+00
  bond pdb=" N   ILE A 301 "
       pdb=" CA  ILE A 301 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.033 1.22e-02 6.72e+03 7.53e+00
  bond pdb=" N   TYR B 304 "
       pdb=" CA  TYR B 304 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.16e-02 7.43e+03 6.51e+00
  bond pdb=" N   THR A 306 "
       pdb=" CA  THR A 306 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.19e+00
  bond pdb=" N   TYR A 304 "
       pdb=" CA  TYR A 304 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.19e-02 7.06e+03 5.96e+00
  ... (remaining 7411 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.93: 9846
        3.93 -     7.86: 224
        7.86 -    11.79: 30
       11.79 -    15.72: 3
       15.72 -    19.66: 1
  Bond angle restraints: 10104
  Sorted by residual:
  angle pdb=" C   PHE B 308 "
        pdb=" N   SER B 309 "
        pdb=" CA  SER B 309 "
      ideal   model   delta    sigma   weight residual
     121.54  141.20  -19.66 1.91e+00 2.74e-01 1.06e+02
  angle pdb=" N   ILE C 357 "
        pdb=" CA  ILE C 357 "
        pdb=" C   ILE C 357 "
      ideal   model   delta    sigma   weight residual
     113.53  106.04    7.49 9.80e-01 1.04e+00 5.84e+01
  angle pdb=" N   ILE A 357 "
        pdb=" CA  ILE A 357 "
        pdb=" C   ILE A 357 "
      ideal   model   delta    sigma   weight residual
     113.53  106.08    7.45 9.80e-01 1.04e+00 5.79e+01
  angle pdb=" N   ILE B 357 "
        pdb=" CA  ILE B 357 "
        pdb=" C   ILE B 357 "
      ideal   model   delta    sigma   weight residual
     113.53  106.11    7.42 9.80e-01 1.04e+00 5.73e+01
  angle pdb=" C   GLN C  16 "
        pdb=" N   SER C  17 "
        pdb=" CA  SER C  17 "
      ideal   model   delta    sigma   weight residual
     120.68  131.37  -10.69 1.52e+00 4.33e-01 4.94e+01
  ... (remaining 10099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.02: 3704
       11.02 -    22.03: 422
       22.03 -    33.05: 154
       33.05 -    44.06: 65
       44.06 -    55.08: 14
  Dihedral angle restraints: 4359
    sinusoidal: 1596
      harmonic: 2763
  Sorted by residual:
  dihedral pdb=" CA  PRO B  96 "
           pdb=" C   PRO B  96 "
           pdb=" N   ASN B  97 "
           pdb=" CA  ASN B  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.05  -27.95     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  PRO A  96 "
           pdb=" C   PRO A  96 "
           pdb=" N   ASN A  97 "
           pdb=" CA  ASN A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.06  -27.94     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  PRO C  96 "
           pdb=" C   PRO C  96 "
           pdb=" N   ASN C  97 "
           pdb=" CA  ASN C  97 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.13  -27.87     0      5.00e+00 4.00e-02 3.11e+01
  ... (remaining 4356 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1037
       0.088 -    0.176: 193
       0.176 -    0.264: 12
       0.264 -    0.352: 3
       0.352 -    0.441: 3
  Chirality restraints: 1248
  Sorted by residual:
  chirality pdb=" CB  ILE A 361 "
            pdb=" CA  ILE A 361 "
            pdb=" CG1 ILE A 361 "
            pdb=" CG2 ILE A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.44 2.00e-01 2.50e+01 4.85e+00
  chirality pdb=" CB  ILE C 361 "
            pdb=" CA  ILE C 361 "
            pdb=" CG1 ILE C 361 "
            pdb=" CG2 ILE C 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.20    0.44 2.00e-01 2.50e+01 4.84e+00
  chirality pdb=" CB  ILE B 361 "
            pdb=" CA  ILE B 361 "
            pdb=" CG1 ILE B 361 "
            pdb=" CG2 ILE B 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.81e+00
  ... (remaining 1245 not shown)

  Planarity restraints: 1236
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 329 "    0.055 5.00e-02 4.00e+02   8.26e-02 1.09e+01
        pdb=" N   PRO C 330 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO C 330 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C 330 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 329 "   -0.055 5.00e-02 4.00e+02   8.24e-02 1.09e+01
        pdb=" N   PRO B 330 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO B 330 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 330 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 329 "    0.055 5.00e-02 4.00e+02   8.24e-02 1.09e+01
        pdb=" N   PRO A 330 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 330 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 330 "    0.047 5.00e-02 4.00e+02
  ... (remaining 1233 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1459
        2.77 -     3.30: 6805
        3.30 -     3.83: 11453
        3.83 -     4.37: 13588
        4.37 -     4.90: 23044
  Nonbonded interactions: 56349
  Sorted by model distance:
  nonbonded pdb=" O   SER C 309 "
            pdb=" N   GLY C 312 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" O   SER A  43 "
            pdb=" OG  SER A  43 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" O   SER B  43 "
            pdb=" OG  SER B  43 "
     model   vdw
     2.398 3.040
  nonbonded pdb=" O   SER C  43 "
            pdb=" OG  SER C  43 "
     model   vdw
     2.399 3.040
  nonbonded pdb=" CZ  PHE B 308 "
            pdb=" O   GLY B 312 "
     model   vdw
     2.414 3.340
  ... (remaining 56344 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.700
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
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      :  0.010   0.078   7416  Z= 0.624
  Angle     :  1.423  19.656  10104  Z= 0.759
  Chirality :  0.071   0.441   1248
  Planarity :  0.010   0.083   1236
  Dihedral  : 12.312  55.076   2595
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 12.42 %
    Favored  : 86.96 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.98 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -7.38 (0.15), residues: 966
  helix: -4.67 (0.08), residues: 663
  sheet:  None (None), residues: 0
  loop : -4.90 (0.27), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 267 
 HIS   0.003   0.001   HIS B 291 
 PHE   0.045   0.004   PHE B  22 
 TYR   0.016   0.003   TYR B 132 
 ARG   0.006   0.001   ARG C 269 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 258
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 SER cc_start: 0.8888 (t) cc_final: 0.8587 (m)
REVERT: A   92 LEU cc_start: 0.7902 (tp) cc_final: 0.7657 (tt)
REVERT: A  104 LEU cc_start: 0.8688 (tt) cc_final: 0.8479 (tt)
REVERT: A  212 TRP cc_start: 0.5837 (t60) cc_final: 0.5250 (t-100)
REVERT: B    1 MET cc_start: 0.2230 (tmt) cc_final: 0.1913 (mtt)
REVERT: B   57 THR cc_start: 0.8349 (m) cc_final: 0.8122 (p)
REVERT: B  274 ARG cc_start: 0.6893 (mtt180) cc_final: 0.6467 (mmt180)
REVERT: B  298 LEU cc_start: 0.8440 (tm) cc_final: 0.8145 (tp)
REVERT: C   10 ASP cc_start: 0.7861 (t0) cc_final: 0.7489 (t70)
REVERT: C   66 ASN cc_start: 0.7153 (p0) cc_final: 0.6714 (p0)
REVERT: C   79 ILE cc_start: 0.9154 (mm) cc_final: 0.8954 (mp)
REVERT: C  135 TRP cc_start: 0.7974 (p90) cc_final: 0.7697 (p90)
REVERT: C  157 ILE cc_start: 0.8380 (tt) cc_final: 0.8130 (tt)
REVERT: C  272 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7608 (tm-30)
  outliers start: 10
  outliers final: 1
  residues processed: 264
  average time/residue: 0.1855
  time to fit residues: 65.6026
Evaluate side-chains
  186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  308 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
A 291 HIS
A 340 ASN
B 291 HIS
C 160 ASN
C 291 HIS
C 303 HIS
C 340 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115785 restraints weight = 10773.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.115016 restraints weight = 7567.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.116393 restraints weight = 6719.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7416  Z= 0.229
  Angle     :  0.887  13.827  10104  Z= 0.440
  Chirality :  0.047   0.293   1248
  Planarity :  0.007   0.071   1236
  Dihedral  :  6.597  36.536   1028
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 14.45 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.78 (0.20), residues: 966
  helix: -3.46 (0.14), residues: 648
  sheet:  None (None), residues: 0
  loop : -4.29 (0.28), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 135 
 HIS   0.002   0.001   HIS A 303 
 PHE   0.025   0.001   PHE C 364 
 TYR   0.013   0.001   TYR B 132 
 ARG   0.007   0.001   ARG C  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 192
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7003 (p)
REVERT: A  104 LEU cc_start: 0.8642 (tt) cc_final: 0.8296 (tt)
REVERT: A  162 ARG cc_start: 0.7952 (tpt90) cc_final: 0.7744 (tpt90)
REVERT: B   44 THR cc_start: 0.9203 (t) cc_final: 0.8648 (m)
REVERT: B  238 LYS cc_start: 0.8541 (mttt) cc_final: 0.8324 (mttp)
REVERT: B  250 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7991 (pp)
REVERT: B  274 ARG cc_start: 0.6900 (mtt180) cc_final: 0.6617 (mmt180)
REVERT: B  298 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8144 (tp)
REVERT: C   10 ASP cc_start: 0.7541 (t0) cc_final: 0.7175 (t70)
REVERT: C   24 ILE cc_start: 0.8616 (pp) cc_final: 0.8377 (mm)
REVERT: C   90 PHE cc_start: 0.6171 (m-10) cc_final: 0.5683 (m-80)
REVERT: C  135 TRP cc_start: 0.7986 (p90) cc_final: 0.7784 (p90)
REVERT: C  258 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7279 (tp)
REVERT: C  272 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7617 (tm-30)
  outliers start: 44
  outliers final: 21
  residues processed: 222
  average time/residue: 0.1560
  time to fit residues: 48.7362
Evaluate side-chains
  196 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  158 TYR
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  370 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0040
   chunk 74 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    7.9990
   chunk 19 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0670
   overall best weight:    0.4130

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 220 GLN
C 291 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.145794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.116398 restraints weight = 10930.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.118632 restraints weight = 7304.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.118877 restraints weight = 6084.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7416  Z= 0.188
  Angle     :  0.813  11.063  10104  Z= 0.393
  Chirality :  0.044   0.168   1248
  Planarity :  0.006   0.069   1236
  Dihedral  :  5.734  21.625   1026
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.39 %
    Favored  : 88.61 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 17.97 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.86 (0.22), residues: 966
  helix: -2.56 (0.17), residues: 627
  sheet:  None (None), residues: 0
  loop : -4.36 (0.26), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 135 
 HIS   0.003   0.001   HIS C 291 
 PHE   0.013   0.001   PHE C 364 
 TYR   0.007   0.001   TYR B 132 
 ARG   0.002   0.000   ARG B 252 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 188
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: A   68 THR cc_start: 0.7457 (t) cc_final: 0.7024 (p)
REVERT: A  259 MET cc_start: 0.7700 (ttm) cc_final: 0.7352 (ttm)
REVERT: A  298 LEU cc_start: 0.8764 (tp) cc_final: 0.8555 (tp)
REVERT: B   44 THR cc_start: 0.9195 (t) cc_final: 0.8603 (m)
REVERT: B  159 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8190 (mt)
REVERT: B  274 ARG cc_start: 0.6722 (mtt180) cc_final: 0.6483 (mmt180)
REVERT: B  298 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8063 (tp)
REVERT: C   10 ASP cc_start: 0.7441 (t0) cc_final: 0.7065 (t70)
REVERT: C   90 PHE cc_start: 0.6144 (m-10) cc_final: 0.5591 (m-10)
REVERT: C  212 TRP cc_start: 0.6614 (t60) cc_final: 0.5638 (t-100)
REVERT: C  248 ASP cc_start: 0.7437 (t0) cc_final: 0.7065 (m-30)
REVERT: C  272 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7621 (tm-30)
  outliers start: 34
  outliers final: 19
  residues processed: 210
  average time/residue: 0.1602
  time to fit residues: 47.5399
Evaluate side-chains
  186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 165
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  220 GLN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  316 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 86 optimal weight:    9.9990
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 84 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
C 291 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.142272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.113757 restraints weight = 10896.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113927 restraints weight = 11282.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.115115 restraints weight = 8956.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7416  Z= 0.317
  Angle     :  0.867  11.321  10104  Z= 0.419
  Chirality :  0.048   0.219   1248
  Planarity :  0.006   0.067   1236
  Dihedral  :  5.859  20.845   1026
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 18.23 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.45 (0.23), residues: 966
  helix: -2.17 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -4.54 (0.26), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP C 135 
 HIS   0.003   0.001   HIS C 291 
 PHE   0.024   0.002   PHE C   7 
 TYR   0.012   0.002   TYR C 140 
 ARG   0.005   0.001   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 188
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8058 (tp)
REVERT: A   96 PRO cc_start: 0.7263 (Cg_exo) cc_final: 0.7055 (Cg_endo)
REVERT: A  156 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7880 (m-40)
REVERT: A  240 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8125 (mm-30)
REVERT: A  272 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7729 (tm-30)
REVERT: A  298 LEU cc_start: 0.8756 (tp) cc_final: 0.8543 (tp)
REVERT: B  264 MET cc_start: 0.8261 (ptm) cc_final: 0.8040 (ptp)
REVERT: B  274 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6478 (mmt180)
REVERT: B  298 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7940 (tp)
REVERT: B  310 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8159 (tm)
REVERT: C   10 ASP cc_start: 0.7504 (t0) cc_final: 0.7234 (t70)
REVERT: C   90 PHE cc_start: 0.6382 (m-10) cc_final: 0.5965 (m-10)
REVERT: C  132 TYR cc_start: 0.8380 (p90) cc_final: 0.8159 (p90)
REVERT: C  258 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7564 (tm)
REVERT: C  272 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7697 (tm-30)
REVERT: C  274 ARG cc_start: 0.6943 (mtt180) cc_final: 0.6710 (mmt180)
  outliers start: 42
  outliers final: 22
  residues processed: 213
  average time/residue: 0.1735
  time to fit residues: 50.9557
Evaluate side-chains
  200 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 173
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  370 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 86 optimal weight:    9.9990
   chunk 74 optimal weight:    0.4980
   chunk 85 optimal weight:    0.5980
   chunk 58 optimal weight:    9.9990
   chunk 36 optimal weight:    0.0020
   chunk 51 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   chunk 70 optimal weight:    0.3980
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
C 291 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.145995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116435 restraints weight = 10740.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.116991 restraints weight = 8456.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.117827 restraints weight = 7855.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7416  Z= 0.182
  Angle     :  0.797  12.997  10104  Z= 0.374
  Chirality :  0.043   0.153   1248
  Planarity :  0.006   0.066   1236
  Dihedral  :  5.304  20.311   1026
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 22.27 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.24), residues: 966
  helix: -1.80 (0.19), residues: 684
  sheet:  None (None), residues: 0
  loop : -4.78 (0.27), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 291 
 PHE   0.013   0.001   PHE C   7 
 TYR   0.006   0.001   TYR B 132 
 ARG   0.002   0.000   ARG A 333 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 188
  time to evaluate  : 0.814 
Fit side-chains
REVERT: A   68 THR cc_start: 0.7714 (OUTLIER) cc_final: 0.7348 (p)
REVERT: A  156 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7827 (m-40)
REVERT: A  217 GLU cc_start: 0.7755 (tp30) cc_final: 0.7450 (tp30)
REVERT: A  250 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8428 (pp)
REVERT: A  259 MET cc_start: 0.7334 (ttm) cc_final: 0.7086 (mtp)
REVERT: A  272 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7692 (tm-30)
REVERT: A  298 LEU cc_start: 0.8603 (tp) cc_final: 0.8351 (tp)
REVERT: B   60 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8390 (mtm)
REVERT: B   95 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7430 (mp)
REVERT: B  259 MET cc_start: 0.7007 (mmt) cc_final: 0.6700 (mtp)
REVERT: B  274 ARG cc_start: 0.6744 (mtt180) cc_final: 0.6394 (mmt180)
REVERT: C   10 ASP cc_start: 0.7531 (t0) cc_final: 0.7200 (t70)
REVERT: C   90 PHE cc_start: 0.6276 (m-10) cc_final: 0.5869 (m-10)
REVERT: C  212 TRP cc_start: 0.6497 (t60) cc_final: 0.5920 (t60)
REVERT: C  272 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: C  308 PHE cc_start: 0.7066 (t80) cc_final: 0.6753 (t80)
  outliers start: 34
  outliers final: 16
  residues processed: 205
  average time/residue: 0.1535
  time to fit residues: 44.3569
Evaluate side-chains
  192 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  310 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 71 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0570
   overall best weight:    1.3904

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

Flipped N/Q/H residues before XYZ refinement:
C 291 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.114551 restraints weight = 10803.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.113858 restraints weight = 9222.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.114783 restraints weight = 8494.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.5421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7416  Z= 0.219
  Angle     :  0.789  11.598  10104  Z= 0.373
  Chirality :  0.044   0.181   1248
  Planarity :  0.005   0.066   1236
  Dihedral  :  5.233  21.752   1026
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 21.61 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.25), residues: 966
  helix: -1.57 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -4.56 (0.26), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 291 
 PHE   0.018   0.001   PHE B  76 
 TYR   0.009   0.001   TYR B 132 
 ARG   0.002   0.000   ARG B 333 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 182
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A  156 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7896 (m-40)
REVERT: A  212 TRP cc_start: 0.6323 (t60) cc_final: 0.5551 (t-100)
REVERT: A  217 GLU cc_start: 0.7828 (tp30) cc_final: 0.7500 (tp30)
REVERT: A  250 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8490 (pp)
REVERT: A  272 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7720 (tm-30)
REVERT: A  298 LEU cc_start: 0.8547 (tp) cc_final: 0.8266 (tp)
REVERT: B   60 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8487 (mtm)
REVERT: B  250 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8321 (pp)
REVERT: B  274 ARG cc_start: 0.6852 (mtt180) cc_final: 0.6532 (mmt180)
REVERT: B  289 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8236 (mp)
REVERT: C   10 ASP cc_start: 0.7632 (t0) cc_final: 0.7260 (t70)
REVERT: C   90 PHE cc_start: 0.6343 (m-10) cc_final: 0.5948 (m-10)
REVERT: C  272 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7713 (tm-30)
REVERT: C  274 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6678 (mmt180)
REVERT: C  308 PHE cc_start: 0.7177 (t80) cc_final: 0.6875 (t80)
  outliers start: 33
  outliers final: 22
  residues processed: 198
  average time/residue: 0.1624
  time to fit residues: 44.2494
Evaluate side-chains
  200 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 173
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    8 LEU
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  313 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 36 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.139849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.111510 restraints weight = 10785.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.111391 restraints weight = 11710.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.112697 restraints weight = 9446.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.5904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7416  Z= 0.339
  Angle     :  0.854  12.418  10104  Z= 0.409
  Chirality :  0.048   0.171   1248
  Planarity :  0.006   0.064   1236
  Dihedral  :  5.583  25.800   1026
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.32 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 20.83 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.25), residues: 966
  helix: -1.63 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -4.20 (0.28), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 135 
 HIS   0.001   0.000   HIS C 291 
 PHE   0.013   0.002   PHE A  22 
 TYR   0.010   0.002   TYR C 140 
 ARG   0.003   0.000   ARG A 162 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  156 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7994 (m-40)
REVERT: A  165 LYS cc_start: 0.5458 (mtmt) cc_final: 0.5166 (mptt)
REVERT: A  212 TRP cc_start: 0.6477 (t60) cc_final: 0.6151 (t60)
REVERT: A  250 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8344 (pp)
REVERT: A  272 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7810 (tm-30)
REVERT: A  298 LEU cc_start: 0.8544 (tp) cc_final: 0.8304 (tp)
REVERT: B   60 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8374 (mtm)
REVERT: B   95 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7587 (mp)
REVERT: B  250 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8373 (pp)
REVERT: B  274 ARG cc_start: 0.6930 (mtt180) cc_final: 0.6590 (mmt180)
REVERT: C  272 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7713 (tm-30)
REVERT: C  274 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6948 (mmt180)
REVERT: C  308 PHE cc_start: 0.7477 (t80) cc_final: 0.7242 (t80)
  outliers start: 40
  outliers final: 27
  residues processed: 195
  average time/residue: 0.1669
  time to fit residues: 44.8373
Evaluate side-chains
  202 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 170
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  156 ASN
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   82 ILE
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  313 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 291 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.143915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.114571 restraints weight = 10875.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.116079 restraints weight = 9292.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.116422 restraints weight = 8535.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.6114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7416  Z= 0.190
  Angle     :  0.783  13.411  10104  Z= 0.368
  Chirality :  0.044   0.156   1248
  Planarity :  0.006   0.065   1236
  Dihedral  :  5.178  22.015   1026
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 23.57 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.26), residues: 966
  helix: -1.28 (0.20), residues: 666
  sheet:  None (None), residues: 0
  loop : -4.45 (0.26), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 135 
 HIS   0.001   0.000   HIS A 291 
 PHE   0.012   0.001   PHE C   7 
 TYR   0.009   0.001   TYR B 132 
 ARG   0.006   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 177
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 LYS cc_start: 0.5674 (mtmt) cc_final: 0.5368 (mptt)
REVERT: A  250 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8358 (pp)
REVERT: A  272 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: A  298 LEU cc_start: 0.8331 (tp) cc_final: 0.8065 (tp)
REVERT: B   60 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8291 (mtm)
REVERT: B   95 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7562 (mp)
REVERT: B  250 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8183 (pp)
REVERT: B  274 ARG cc_start: 0.6840 (mtt180) cc_final: 0.6551 (mmt180)
REVERT: C   90 PHE cc_start: 0.6746 (m-80) cc_final: 0.6386 (m-10)
REVERT: C  274 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6809 (mmt180)
REVERT: C  308 PHE cc_start: 0.7389 (t80) cc_final: 0.7144 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 193
  average time/residue: 0.1683
  time to fit residues: 45.0812
Evaluate side-chains
  194 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 171
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   49 MET
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  360 CYS
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 27 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.145768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.116401 restraints weight = 10839.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.116130 restraints weight = 9076.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.116592 restraints weight = 9667.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.6273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7416  Z= 0.191
  Angle     :  0.781  13.295  10104  Z= 0.366
  Chirality :  0.045   0.177   1248
  Planarity :  0.005   0.062   1236
  Dihedral  :  5.039  22.473   1026
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 23.18 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.26), residues: 966
  helix: -1.09 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -4.40 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 135 
 HIS   0.001   0.000   HIS A 291 
 PHE   0.020   0.001   PHE B 308 
 TYR   0.007   0.001   TYR C 344 
 ARG   0.006   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 180
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 LYS cc_start: 0.5633 (mtmt) cc_final: 0.5298 (mptt)
REVERT: A  212 TRP cc_start: 0.6414 (t60) cc_final: 0.6105 (t60)
REVERT: A  219 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9070 (tt)
REVERT: A  250 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8367 (pp)
REVERT: A  272 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7801 (tm-30)
REVERT: A  298 LEU cc_start: 0.8275 (tp) cc_final: 0.8010 (tp)
REVERT: B   60 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8327 (mtm)
REVERT: B   95 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7561 (mp)
REVERT: B  250 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8245 (pp)
REVERT: B  274 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6494 (mmt180)
REVERT: C   90 PHE cc_start: 0.6934 (m-80) cc_final: 0.6527 (m-10)
REVERT: C  274 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6722 (mmt180)
REVERT: C  308 PHE cc_start: 0.7381 (t80) cc_final: 0.7091 (t80)
  outliers start: 31
  outliers final: 19
  residues processed: 198
  average time/residue: 0.1733
  time to fit residues: 47.0716
Evaluate side-chains
  197 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0270
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 82 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0070
   chunk 36 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.3856

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.147908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.112883 restraints weight = 10898.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.115753 restraints weight = 6579.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.117467 restraints weight = 4922.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.6403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7416  Z= 0.172
  Angle     :  0.780  13.545  10104  Z= 0.362
  Chirality :  0.043   0.163   1248
  Planarity :  0.005   0.063   1236
  Dihedral  :  4.869  23.719   1026
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 25.00 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.26), residues: 966
  helix: -0.93 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -4.36 (0.26), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 291 
 PHE   0.017   0.001   PHE B 308 
 TYR   0.007   0.001   TYR C 132 
 ARG   0.006   0.000   ARG A  89 

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

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

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1932 Ramachandran restraints generated.
    966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 179
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 ASP cc_start: 0.7925 (t0) cc_final: 0.7709 (t0)
REVERT: A  165 LYS cc_start: 0.5567 (mtmt) cc_final: 0.5247 (mptt)
REVERT: A  212 TRP cc_start: 0.6377 (t60) cc_final: 0.6057 (t60)
REVERT: A  219 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8905 (tt)
REVERT: A  250 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8293 (pp)
REVERT: A  272 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7837 (tm-30)
REVERT: A  298 LEU cc_start: 0.8139 (tp) cc_final: 0.7903 (tp)
REVERT: B   60 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8273 (mtm)
REVERT: B  250 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8207 (pp)
REVERT: B  274 ARG cc_start: 0.6828 (mtt180) cc_final: 0.6514 (mmt180)
REVERT: C   90 PHE cc_start: 0.6917 (m-80) cc_final: 0.6492 (m-10)
REVERT: C  212 TRP cc_start: 0.6907 (t60) cc_final: 0.6608 (t60)
REVERT: C  274 ARG cc_start: 0.7037 (mtt180) cc_final: 0.6683 (mmt180)
  outliers start: 23
  outliers final: 17
  residues processed: 192
  average time/residue: 0.1859
  time to fit residues: 49.2937
Evaluate side-chains
  196 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  248 ASP
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  313 VAL
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue  153 VAL
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  314 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 16 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 64 optimal weight:    9.9990
   chunk 62 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0060
   overall best weight:    0.4396

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.148220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.113847 restraints weight = 10668.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116649 restraints weight = 6479.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.118272 restraints weight = 4860.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.6526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7416  Z= 0.174
  Angle     :  0.781  12.440  10104  Z= 0.361
  Chirality :  0.044   0.191   1248
  Planarity :  0.005   0.061   1236
  Dihedral  :  4.704  22.187   1026
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 26.43 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.27), residues: 966
  helix: -0.60 (0.21), residues: 657
  sheet:  None (None), residues: 0
  loop : -4.28 (0.27), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 135 
 HIS   0.001   0.000   HIS C 291 
 PHE   0.017   0.001   PHE B 308 
 TYR   0.006   0.001   TYR C 344 
 ARG   0.006   0.000   ARG A  89 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2274.65 seconds
wall clock time: 41 minutes 25.42 seconds (2485.42 seconds total)