Starting phenix.real_space_refine
on Wed Sep 17 08:22:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7cye_30498/09_2025/7cye_30498_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7cye_30498/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7cye_30498/09_2025/7cye_30498_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7cye_30498/09_2025/7cye_30498_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7cye_30498/09_2025/7cye_30498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7cye_30498/09_2025/7cye_30498.map"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.90, per 1000 atoms: 0.26
  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: 0.58
  Conformation dependent library (CDL) restraints added in 423.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.20
  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: 0.95

  Time building geometry restraints manager: 0.80 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.270
  Find NCS groups from input model:        0.060
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.380
-------------------------------------------------------------------------------
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= 0.415
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.006   0.001   ARG C 269 
 TYR   0.016   0.003   TYR B 132 
 PHE   0.045   0.004   PHE B  22 
 TRP   0.010   0.002   TRP C 267 
 HIS   0.003   0.001   HIS B 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00965 ( 7416)
  covalent geometry    : angle       1.42265 (10104)
  hydrogen bonds       : bond        0.29750 (  267)
  hydrogen bonds       : angle      10.87114 (  756)

*********************** 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  : 0.282 
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: 0.0876
  time to fit residues: 31.2532
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  : 0.271 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0670
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 220 GLN
C 291 HIS
C 303 HIS
C 340 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.142957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.114667 restraints weight = 10925.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113913 restraints weight = 7991.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.115190 restraints weight = 7059.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.115472 restraints weight = 5722.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.116178 restraints weight = 5383.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7416  Z= 0.164
  Angle     :  0.896  13.566  10104  Z= 0.444
  Chirality :  0.047   0.295   1248
  Planarity :  0.008   0.072   1236
  Dihedral  :  6.658  37.743   1028
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.46 %
    Favored  : 89.54 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 14.84 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.84 (0.19), residues: 966
  helix: -3.52 (0.14), residues: 648
  sheet:  None (None), residues: 0
  loop : -4.30 (0.28), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  89 
 TYR   0.011   0.001   TYR B 132 
 PHE   0.025   0.001   PHE C 364 
 TRP   0.022   0.001   TRP A 135 
 HIS   0.001   0.000   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7416)
  covalent geometry    : angle       0.89569 (10104)
  hydrogen bonds       : bond        0.05297 (  267)
  hydrogen bonds       : angle       5.10731 (  756)

*********************** 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
  230 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 189
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7009 (p)
REVERT: A  104 LEU cc_start: 0.8647 (tt) cc_final: 0.8308 (tt)
REVERT: B   44 THR cc_start: 0.9190 (t) cc_final: 0.8513 (m)
REVERT: B   70 MET cc_start: 0.8366 (ttm) cc_final: 0.8107 (ttm)
REVERT: B  250 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8060 (pp)
REVERT: B  274 ARG cc_start: 0.6891 (mtt180) cc_final: 0.6629 (mmt180)
REVERT: B  298 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8167 (tp)
REVERT: C   10 ASP cc_start: 0.7532 (t0) cc_final: 0.7213 (t70)
REVERT: C   24 ILE cc_start: 0.8631 (pp) cc_final: 0.8354 (mm)
REVERT: C   90 PHE cc_start: 0.6230 (m-10) cc_final: 0.5729 (m-80)
REVERT: C  135 TRP cc_start: 0.7974 (p90) cc_final: 0.7755 (p90)
REVERT: C  258 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7185 (tp)
REVERT: C  272 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7603 (tm-30)
  outliers start: 41
  outliers final: 21
  residues processed: 218
  average time/residue: 0.0672
  time to fit residues: 20.8797
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  : 0.263 
-------------------------------------------------------------------------------
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 78 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 86 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 62 optimal weight:    0.2980
   chunk 13 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.143150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.114279 restraints weight = 10911.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.114519 restraints weight = 7571.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.115567 restraints weight = 7758.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.115849 restraints weight = 5868.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116067 restraints weight = 5929.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7416  Z= 0.149
  Angle     :  0.823  10.651  10104  Z= 0.399
  Chirality :  0.045   0.170   1248
  Planarity :  0.006   0.069   1236
  Dihedral  :  5.859  21.751   1026
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.87 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 17.19 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.91 (0.22), residues: 966
  helix: -2.59 (0.17), residues: 630
  sheet:  None (None), residues: 0
  loop : -4.41 (0.26), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 162 
 TYR   0.009   0.001   TYR B 140 
 PHE   0.014   0.001   PHE B  22 
 TRP   0.016   0.001   TRP A 135 
 HIS   0.003   0.001   HIS C 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7416)
  covalent geometry    : angle       0.82304 (10104)
  hydrogen bonds       : bond        0.04049 (  267)
  hydrogen bonds       : angle       4.21491 (  756)

*********************** 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
  226 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 185
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 THR cc_start: 0.7525 (t) cc_final: 0.7105 (p)
REVERT: A  259 MET cc_start: 0.7752 (ttm) cc_final: 0.7382 (ttm)
REVERT: A  298 LEU cc_start: 0.8788 (tp) cc_final: 0.8573 (tp)
REVERT: B    1 MET cc_start: 0.4027 (mmm) cc_final: 0.3784 (mmm)
REVERT: B  144 ASP cc_start: 0.8125 (t0) cc_final: 0.7832 (t0)
REVERT: B  274 ARG cc_start: 0.6753 (mtt180) cc_final: 0.6451 (mmt180)
REVERT: B  298 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8048 (tp)
REVERT: C   10 ASP cc_start: 0.7506 (t0) cc_final: 0.7157 (t70)
REVERT: C   90 PHE cc_start: 0.6200 (m-10) cc_final: 0.5645 (m-10)
REVERT: C  212 TRP cc_start: 0.6608 (t60) cc_final: 0.5643 (t-100)
REVERT: C  248 ASP cc_start: 0.7435 (t0) cc_final: 0.6779 (m-30)
REVERT: C  272 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7665 (tm-30)
  outliers start: 41
  outliers final: 23
  residues processed: 210
  average time/residue: 0.0681
  time to fit residues: 20.5893
Evaluate side-chains
  185 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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   74 VAL
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    4 LEU
Chi-restraints excluded: chain B residue   82 ILE
Chi-restraints excluded: chain B residue   85 VAL
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   95 LEU
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  294 ILE
Chi-restraints excluded: chain C residue  313 VAL
Chi-restraints excluded: chain C residue  316 LEU
Chi-restraints excluded: chain C residue  370 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3663 r_free = 0.3663 target = 0.146356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.117432 restraints weight = 10980.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.117224 restraints weight = 9449.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.118559 restraints weight = 7945.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.119078 restraints weight = 5956.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.119582 restraints weight = 5955.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.4208

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= 0.131
  Angle     :  0.803  13.910  10104  Z= 0.382
  Chirality :  0.044   0.171   1248
  Planarity :  0.006   0.067   1236
  Dihedral  :  5.414  20.731   1026
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 19.14 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.39 (0.24), residues: 966
  helix: -2.11 (0.19), residues: 651
  sheet:  None (None), residues: 0
  loop : -4.49 (0.27), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  89 
 TYR   0.007   0.001   TYR A 132 
 PHE   0.023   0.001   PHE C   7 
 TRP   0.024   0.001   TRP C 135 
 HIS   0.002   0.000   HIS C 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7416)
  covalent geometry    : angle       0.80301 (10104)
  hydrogen bonds       : bond        0.03373 (  267)
  hydrogen bonds       : angle       3.81593 (  756)

*********************** 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
  215 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 177
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.7200 (p)
REVERT: A   70 MET cc_start: 0.7549 (ttm) cc_final: 0.7344 (ttm)
REVERT: A   96 PRO cc_start: 0.7209 (Cg_exo) cc_final: 0.7000 (Cg_endo)
REVERT: A  156 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7850 (m-40)
REVERT: A  272 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: A  298 LEU cc_start: 0.8702 (tp) cc_final: 0.8480 (tp)
REVERT: B    1 MET cc_start: 0.3837 (mmm) cc_final: 0.3598 (mmm)
REVERT: B   70 MET cc_start: 0.8441 (ttm) cc_final: 0.8206 (ttm)
REVERT: B  159 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8136 (mt)
REVERT: B  274 ARG cc_start: 0.6680 (mtt180) cc_final: 0.6477 (mmt180)
REVERT: B  298 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8041 (tp)
REVERT: C   10 ASP cc_start: 0.7481 (t0) cc_final: 0.7107 (t70)
REVERT: C   90 PHE cc_start: 0.6231 (m-10) cc_final: 0.5842 (m-10)
REVERT: C  212 TRP cc_start: 0.6582 (t60) cc_final: 0.5777 (t-100)
REVERT: C  272 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7723 (tm-30)
REVERT: C  300 MET cc_start: 0.8678 (mmt) cc_final: 0.8315 (mmm)
  outliers start: 38
  outliers final: 21
  residues processed: 200
  average time/residue: 0.0751
  time to fit residues: 21.0346
Evaluate side-chains
  187 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 162
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
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   68 THR
Chi-restraints excluded: chain A residue  156 ASN
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  327 SER
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    8 LEU
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   95 LEU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  298 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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 94 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 62 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    2.3588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.141874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.113049 restraints weight = 10832.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.112871 restraints weight = 10757.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.114445 restraints weight = 8119.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.115441 restraints weight = 6023.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.116023 restraints weight = 5691.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7416  Z= 0.189
  Angle     :  0.838  12.849  10104  Z= 0.400
  Chirality :  0.047   0.165   1248
  Planarity :  0.006   0.066   1236
  Dihedral  :  5.669  20.316   1026
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 20.05 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.06 (0.24), residues: 966
  helix: -1.86 (0.19), residues: 645
  sheet:  None (None), residues: 0
  loop : -4.31 (0.25), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 333 
 TYR   0.011   0.002   TYR C 140 
 PHE   0.014   0.001   PHE B  22 
 TRP   0.030   0.002   TRP C 135 
 HIS   0.001   0.001   HIS B 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 7416)
  covalent geometry    : angle       0.83793 (10104)
  hydrogen bonds       : bond        0.04096 (  267)
  hydrogen bonds       : angle       3.95382 (  756)

*********************** 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
  235 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 192
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 THR cc_start: 0.7888 (OUTLIER) cc_final: 0.7540 (p)
REVERT: A   96 PRO cc_start: 0.7266 (Cg_exo) cc_final: 0.7059 (Cg_endo)
REVERT: A  156 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7872 (m-40)
REVERT: A  240 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8154 (mm-30)
REVERT: A  250 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8419 (pp)
REVERT: A  259 MET cc_start: 0.7573 (ttm) cc_final: 0.7264 (ttm)
REVERT: A  272 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: A  298 LEU cc_start: 0.8664 (tp) cc_final: 0.8449 (tp)
REVERT: B   70 MET cc_start: 0.8499 (ttm) cc_final: 0.8290 (ttm)
REVERT: B  159 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8106 (mt)
REVERT: B  258 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7520 (tm)
REVERT: B  274 ARG cc_start: 0.6802 (mtt180) cc_final: 0.6420 (mmt180)
REVERT: B  298 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7875 (tp)
REVERT: C   10 ASP cc_start: 0.7563 (t0) cc_final: 0.7292 (t70)
REVERT: C   16 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8744 (mt0)
REVERT: C   90 PHE cc_start: 0.6395 (m-10) cc_final: 0.5988 (m-10)
REVERT: C  272 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7702 (tm-30)
REVERT: C  274 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6718 (mmt180)
  outliers start: 43
  outliers final: 25
  residues processed: 216
  average time/residue: 0.0726
  time to fit residues: 22.1069
Evaluate side-chains
  207 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   80 LEU
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   85 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  159 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  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   16 GLN
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  153 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
Chi-restraints excluded: chain C residue  370 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 94 optimal weight:    0.2980
   chunk 79 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 67 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0030
   chunk 83 optimal weight:    0.0070
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.3608

-------------------------------------------------------------------------------
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 = 0.3663 r_free = 0.3663 target = 0.146487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.117174 restraints weight = 10966.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116601 restraints weight = 9207.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.117733 restraints weight = 8230.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.118551 restraints weight = 6191.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.119115 restraints weight = 5712.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7416  Z= 0.124
  Angle     :  0.763  12.646  10104  Z= 0.360
  Chirality :  0.043   0.151   1248
  Planarity :  0.006   0.066   1236
  Dihedral  :  5.167  20.871   1026
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.69 (0.25), residues: 966
  helix: -1.50 (0.20), residues: 648
  sheet:  None (None), residues: 0
  loop : -4.40 (0.26), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 333 
 TYR   0.007   0.001   TYR B 132 
 PHE   0.014   0.001   PHE B  76 
 TRP   0.016   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7416)
  covalent geometry    : angle       0.76280 (10104)
  hydrogen bonds       : bond        0.03229 (  267)
  hydrogen bonds       : angle       3.66818 (  756)

*********************** 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: 30
    poor density    : 185
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   68 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7393 (p)
REVERT: A  156 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7930 (m-40)
REVERT: A  217 GLU cc_start: 0.7838 (tp30) cc_final: 0.7539 (tp30)
REVERT: A  250 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8372 (pp)
REVERT: A  259 MET cc_start: 0.7286 (ttm) cc_final: 0.7065 (ttm)
REVERT: A  272 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: A  298 LEU cc_start: 0.8452 (tp) cc_final: 0.8196 (tp)
REVERT: B    4 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7335 (mt)
REVERT: B   70 MET cc_start: 0.8509 (ttm) cc_final: 0.8181 (ttm)
REVERT: B   95 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7382 (mp)
REVERT: B  250 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8179 (pp)
REVERT: B  274 ARG cc_start: 0.6789 (mtt180) cc_final: 0.6517 (mmt180)
REVERT: C   10 ASP cc_start: 0.7547 (t0) cc_final: 0.7198 (t70)
REVERT: C   90 PHE cc_start: 0.6348 (m-10) cc_final: 0.5946 (m-10)
REVERT: C  212 TRP cc_start: 0.6633 (t60) cc_final: 0.5829 (t-100)
REVERT: C  272 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: C  308 PHE cc_start: 0.7040 (t80) cc_final: 0.6771 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 207
  average time/residue: 0.0609
  time to fit residues: 18.0930
Evaluate side-chains
  194 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 170
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 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  310 LEU
Chi-restraints excluded: chain A residue  319 ILE
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   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  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   68 THR
Chi-restraints excluded: chain C residue   95 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    0.0070
   chunk 9 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 91 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8002

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.146463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116092 restraints weight = 10727.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.117412 restraints weight = 7767.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.118058 restraints weight = 7059.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.118314 restraints weight = 5717.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.120980 restraints weight = 5121.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.5622

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= 0.126
  Angle     :  0.773  12.743  10104  Z= 0.362
  Chirality :  0.044   0.159   1248
  Planarity :  0.005   0.060   1236
  Dihedral  :  5.057  20.502   1026
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 24.61 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.46 (0.25), residues: 966
  helix: -1.27 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -4.49 (0.25), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  63 
 TYR   0.008   0.001   TYR B 132 
 PHE   0.011   0.001   PHE C   7 
 TRP   0.015   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7416)
  covalent geometry    : angle       0.77340 (10104)
  hydrogen bonds       : bond        0.03287 (  267)
  hydrogen bonds       : angle       3.63950 (  756)

*********************** 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
  202 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 174
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  156 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7974 (m-40)
REVERT: A  212 TRP cc_start: 0.6285 (t60) cc_final: 0.5572 (t-100)
REVERT: A  217 GLU cc_start: 0.7822 (tp30) cc_final: 0.7530 (tp30)
REVERT: A  250 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8403 (pp)
REVERT: A  272 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: A  298 LEU cc_start: 0.8424 (tp) cc_final: 0.8146 (tp)
REVERT: B   70 MET cc_start: 0.8424 (ttm) cc_final: 0.8057 (ttm)
REVERT: B  250 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8270 (pp)
REVERT: B  274 ARG cc_start: 0.6781 (mtt180) cc_final: 0.6548 (mmt180)
REVERT: C   10 ASP cc_start: 0.7579 (t0) cc_final: 0.7238 (t70)
REVERT: C   90 PHE cc_start: 0.6439 (m-10) cc_final: 0.6058 (m-10)
REVERT: C  212 TRP cc_start: 0.6748 (t60) cc_final: 0.5960 (t-100)
  outliers start: 28
  outliers final: 18
  residues processed: 190
  average time/residue: 0.0724
  time to fit residues: 19.3886
Evaluate side-chains
  189 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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  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   92 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  359 VAL
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   60 MET
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  294 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0470
   chunk 73 optimal weight:    0.0070
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0870
   overall best weight:    0.2452

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.150046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.118786 restraints weight = 10754.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.122004 restraints weight = 7353.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.122080 restraints weight = 5358.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.122443 restraints weight = 4550.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.122609 restraints weight = 4238.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.5870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7416  Z= 0.118
  Angle     :  0.753  12.238  10104  Z= 0.351
  Chirality :  0.043   0.151   1248
  Planarity :  0.005   0.061   1236
  Dihedral  :  4.830  20.577   1026
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.63 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 24.61 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.26), residues: 966
  helix: -1.14 (0.21), residues: 660
  sheet:  None (None), residues: 0
  loop : -4.51 (0.25), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  89 
 TYR   0.007   0.001   TYR B 132 
 PHE   0.011   0.001   PHE C   7 
 TRP   0.017   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7416)
  covalent geometry    : angle       0.75274 (10104)
  hydrogen bonds       : bond        0.02948 (  267)
  hydrogen bonds       : angle       3.52341 (  756)

*********************** 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
  204 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   14 GLN cc_start: 0.8148 (tm-30) cc_final: 0.7890 (tm-30)
REVERT: A  101 VAL cc_start: 0.8308 (t) cc_final: 0.8102 (t)
REVERT: A  144 ASP cc_start: 0.8235 (t0) cc_final: 0.7930 (t0)
REVERT: A  156 ASN cc_start: 0.8047 (OUTLIER) cc_final: 0.7724 (m110)
REVERT: A  159 LEU cc_start: 0.7926 (mt) cc_final: 0.7710 (mt)
REVERT: A  212 TRP cc_start: 0.6225 (t60) cc_final: 0.5568 (t-100)
REVERT: A  250 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8245 (pp)
REVERT: A  272 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7796 (tm-30)
REVERT: A  298 LEU cc_start: 0.8263 (tp) cc_final: 0.7998 (tp)
REVERT: B   70 MET cc_start: 0.8439 (ttm) cc_final: 0.8158 (ttm)
REVERT: B  250 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8124 (pp)
REVERT: B  274 ARG cc_start: 0.6777 (mtt180) cc_final: 0.6461 (mmt180)
REVERT: C   10 ASP cc_start: 0.7617 (t0) cc_final: 0.7248 (t70)
REVERT: C   86 PHE cc_start: 0.8024 (m-80) cc_final: 0.7660 (m-80)
REVERT: C   90 PHE cc_start: 0.6465 (m-10) cc_final: 0.6104 (m-10)
REVERT: C  212 TRP cc_start: 0.6643 (t60) cc_final: 0.5893 (t-100)
  outliers start: 25
  outliers final: 14
  residues processed: 195
  average time/residue: 0.0682
  time to fit residues: 18.7738
Evaluate side-chains
  186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 169
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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  250 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  238 LYS
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   49 MET
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  316 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   overall best weight:    1.8984

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.143261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.114223 restraints weight = 10793.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.113948 restraints weight = 9411.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.114904 restraints weight = 8131.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.115485 restraints weight = 6322.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.115751 restraints weight = 6374.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.5990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7416  Z= 0.166
  Angle     :  0.812  13.341  10104  Z= 0.380
  Chirality :  0.046   0.177   1248
  Planarity :  0.005   0.060   1236
  Dihedral  :  5.097  20.467   1026
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.63 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 25.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.09 (0.26), residues: 966
  helix: -1.02 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -4.37 (0.26), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  89 
 TYR   0.009   0.001   TYR C 344 
 PHE   0.009   0.001   PHE B 142 
 TRP   0.017   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 7416)
  covalent geometry    : angle       0.81154 (10104)
  hydrogen bonds       : bond        0.03589 (  267)
  hydrogen bonds       : angle       3.70682 (  756)

*********************** 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
  200 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  156 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7801 (m110)
REVERT: A  212 TRP cc_start: 0.6351 (t60) cc_final: 0.5671 (t-100)
REVERT: A  250 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8523 (pp)
REVERT: A  272 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: A  298 LEU cc_start: 0.8311 (tp) cc_final: 0.8081 (tp)
REVERT: B   70 MET cc_start: 0.8529 (ttm) cc_final: 0.8322 (ttm)
REVERT: B   95 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7470 (mp)
REVERT: B  250 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8420 (pp)
REVERT: B  274 ARG cc_start: 0.6872 (mtt180) cc_final: 0.6506 (mmt180)
REVERT: C   10 ASP cc_start: 0.7691 (t0) cc_final: 0.7363 (t70)
REVERT: C   86 PHE cc_start: 0.8215 (m-80) cc_final: 0.7917 (m-80)
REVERT: C   90 PHE cc_start: 0.6698 (m-10) cc_final: 0.6366 (m-10)
  outliers start: 26
  outliers final: 14
  residues processed: 189
  average time/residue: 0.0692
  time to fit residues: 18.7754
Evaluate side-chains
  191 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
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  250 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  360 CYS
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   36 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   95 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  316 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0870
   chunk 25 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 57 optimal weight:    0.0030
   chunk 45 optimal weight:    0.0870
   chunk 64 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.5748

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.147645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.116634 restraints weight = 10761.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.119354 restraints weight = 7243.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.119550 restraints weight = 5825.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.119978 restraints weight = 4856.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.120137 restraints weight = 4519.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.6201

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= 0.123
  Angle     :  0.787  12.827  10104  Z= 0.363
  Chirality :  0.043   0.156   1248
  Planarity :  0.005   0.063   1236
  Dihedral  :  4.867  22.230   1026
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.21 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 27.47 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.99 (0.26), residues: 966
  helix: -0.92 (0.20), residues: 672
  sheet:  None (None), residues: 0
  loop : -4.47 (0.27), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  89 
 TYR   0.007   0.001   TYR C 344 
 PHE   0.010   0.001   PHE C   7 
 TRP   0.016   0.001   TRP A 135 
 HIS   0.001   0.000   HIS C 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7416)
  covalent geometry    : angle       0.78734 (10104)
  hydrogen bonds       : bond        0.03080 (  267)
  hydrogen bonds       : angle       3.61017 (  756)

********************** 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
  195 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  118 MET cc_start: 0.5179 (mmp) cc_final: 0.4863 (mmp)
REVERT: A  144 ASP cc_start: 0.8276 (t0) cc_final: 0.8063 (t0)
REVERT: A  156 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7714 (m110)
REVERT: A  212 TRP cc_start: 0.6272 (t60) cc_final: 0.5542 (t-100)
REVERT: A  250 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8294 (pp)
REVERT: A  272 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: A  298 LEU cc_start: 0.8200 (tp) cc_final: 0.7955 (tp)
REVERT: B   70 MET cc_start: 0.8469 (ttm) cc_final: 0.8242 (ttm)
REVERT: B  250 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8093 (pp)
REVERT: B  274 ARG cc_start: 0.6819 (mtt180) cc_final: 0.6466 (mmt180)
REVERT: C   86 PHE cc_start: 0.8219 (m-80) cc_final: 0.7853 (m-80)
REVERT: C  212 TRP cc_start: 0.6727 (t60) cc_final: 0.5940 (t-100)
  outliers start: 17
  outliers final: 13
  residues processed: 186
  average time/residue: 0.0711
  time to fit residues: 18.8625
Evaluate side-chains
  185 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
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  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    8 LEU
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  314 VAL
Chi-restraints excluded: chain C residue  316 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 93 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 3 optimal weight:    0.0170
   chunk 9 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7018

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.147691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.116230 restraints weight = 10650.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.119025 restraints weight = 7439.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.119414 restraints weight = 5964.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.119436 restraints weight = 5000.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.119626 restraints weight = 4923.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.6322

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= 0.124
  Angle     :  0.776  12.601  10104  Z= 0.359
  Chirality :  0.044   0.170   1248
  Planarity :  0.005   0.058   1236
  Dihedral  :  4.780  25.256   1026
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 26.95 %
    Favored  : 70.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.26), residues: 966
  helix: -0.65 (0.21), residues: 645
  sheet:  None (None), residues: 0
  loop : -4.16 (0.26), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  89 
 TYR   0.008   0.001   TYR C 344 
 PHE   0.010   0.001   PHE C   7 
 TRP   0.016   0.001   TRP A 135 
 HIS   0.001   0.000   HIS B 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7416)
  covalent geometry    : angle       0.77591 (10104)
  hydrogen bonds       : bond        0.03107 (  267)
  hydrogen bonds       : angle       3.56569 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1243.43 seconds
wall clock time: 22 minutes 9.85 seconds (1329.85 seconds total)