Starting phenix.real_space_refine
on Fri Aug 22 23:46:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j24_35944/08_2025/8j24_35944.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j24_35944/08_2025/8j24_35944.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j24_35944/08_2025/8j24_35944.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j24_35944/08_2025/8j24_35944.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j24_35944/08_2025/8j24_35944.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j24_35944/08_2025/8j24_35944.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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      57      5.16       5
     C    5509      2.51       5
     N    1464      2.21       5
     O    1596      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8626
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2610
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 1690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1690
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "D"
      Number of atoms: 2084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2084
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 14, 'TRANS': 243}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 433
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "G"
      Number of atoms: 1805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1805
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 10, 'TRANS': 224}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'ACT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.25, per 1000 atoms: 0.26
  Number of scatterers: 8626
  At special positions: 0
  Unit cell: (117.52, 106.08, 124.8, 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      57     16.00
     O    1596      8.00
     N    1464      7.00
     C    5509      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  82 " - pdb=" SG  CYS D 164 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  96 " distance=2.03

  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: 0.75
  Conformation dependent library (CDL) restraints added in 472.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2062

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 12 sheets defined
      39.1% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 23
      removed outlier: 3.965A  pdb=" N   ARG B   6 " --> pdb=" O   LEU B   2 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLN B   7 " --> pdb=" O   ASP B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 33
      removed outlier: 3.526A  pdb=" N   ILE B  31 " --> pdb=" O   THR B  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 32
      removed outlier: 3.867A  pdb=" N   ALA C  12 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 52
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 4.467A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 232
      removed outlier: 4.242A  pdb=" N   ASP C 231 " --> pdb=" O   SER C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 255
    Processing helix  chain 'C' and resid 256 through 260
      removed outlier: 3.893A  pdb=" N   THR C 260 " --> pdb=" O   LYS C 257 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 3.693A  pdb=" N   GLU C 276 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 286
      removed outlier: 3.556A  pdb=" N   ILE C 285 " --> pdb=" O   PRO C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 309
    Processing helix  chain 'C' and resid 330 through 351
      removed outlier: 3.879A  pdb=" N   ASP C 341 " --> pdb=" O   ASP C 337 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL C 342 " --> pdb=" O   ALA C 338 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS C 351 " --> pdb=" O   ASN C 347 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 38
      removed outlier: 3.518A  pdb=" N   TYR D  14 " --> pdb=" O   ILE D  10 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ILE D  15 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
      Proline residue:  D  23  - end of helix
    Processing helix  chain 'D' and resid 42 through 61
      removed outlier: 3.799A  pdb=" N   LEU D  61 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 71
    Processing helix  chain 'D' and resid 78 through 113
    Processing helix  chain 'D' and resid 113 through 121
    Processing helix  chain 'D' and resid 122 through 141
      removed outlier: 3.925A  pdb=" N   GLY D 126 " --> pdb=" O   ARG D 122 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 142 through 148
    Processing helix  chain 'D' and resid 172 through 188
      removed outlier: 3.525A  pdb=" N   LEU D 177 " --> pdb=" O   LEU D 173 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
    Processing helix  chain 'D' and resid 188 through 209
    Processing helix  chain 'D' and resid 213 through 249
      removed outlier: 3.560A  pdb=" N   ARG D 219 " --> pdb=" O   GLN D 215 " (cutoff:3.500A)
      Proline residue:  D 237  - end of helix
      removed outlier: 3.856A  pdb=" N   HIS D 242 " --> pdb=" O   TYR D 238 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU D 243 " --> pdb=" O   ASN D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 273
      removed outlier: 3.549A  pdb=" N   PHE D 261 " --> pdb=" O   ILE D 257 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ASN D 265 " --> pdb=" O   PHE D 261 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ALA D 266 " --> pdb=" O   SER D 262 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   SER D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
      Proline residue:  D 270  - end of helix
    Processing helix  chain 'F' and resid 2 through 20
    Processing helix  chain 'F' and resid 25 through 40
    Processing helix  chain 'F' and resid 51 through 55
    Processing helix  chain 'G' and resid 87 through 91
      removed outlier: 3.655A  pdb=" N   THR G  91 " --> pdb=" O   SER G  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 221 through 225
      removed outlier: 3.876A  pdb=" N   VAL G 225 " --> pdb=" O   ALA G 222 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 49
      removed outlier: 6.606A  pdb=" N   ILE B 336 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   THR B  48 " --> pdb=" O   LEU B 334 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LEU B 334 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   CYS B 315 " --> pdb=" O   GLY B 328 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 58
      removed outlier: 6.505A  pdb=" N   ALA B  71 " --> pdb=" O   TYR B  57 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   SER B  72 " --> pdb=" O   LYS B  76 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LYS B  76 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ASP B  81 " --> pdb=" O   LYS B  87 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LYS B  87 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 103
      removed outlier: 6.060A  pdb=" N   CYS B 119 " --> pdb=" O   GLU B 136 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLU B 136 " --> pdb=" O   CYS B 119 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   ILE B 121 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 144 through 149
      removed outlier: 6.332A  pdb=" N   SER B 158 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   CYS B 147 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL B 156 " --> pdb=" O   CYS B 147 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   PHE B 149 " --> pdb=" O   GLN B 154 " (cutoff:3.500A)
      removed outlier: 7.771A  pdb=" N   GLN B 154 " --> pdb=" O   PHE B 149 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASP B 168 " --> pdb=" O   GLN B 174 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   GLN B 174 " --> pdb=" O   ASP B 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 190
      removed outlier: 3.571A  pdb=" N   SER B 187 " --> pdb=" O   GLY B 200 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   SER B 205 " --> pdb=" O   ALA B 201 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ALA B 206 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   THR B 219 " --> pdb=" O   ALA B 206 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU B 208 " --> pdb=" O   ARG B 217 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   MET B 215 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 227 through 232
      removed outlier: 3.507A  pdb=" N   MET B 260 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   ASP B 252 " --> pdb=" O   GLU B 258 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   GLU B 258 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 271 through 276
      removed outlier: 4.123A  pdb=" N   SER B 273 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASP B 296 " --> pdb=" O   ARG B 302 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ARG B 302 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 191
      removed outlier: 6.745A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'G' and resid 11 through 12
      removed outlier: 6.802A  pdb=" N   MET G  34 " --> pdb=" O   TYR G  50 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   TYR G  50 " --> pdb=" O   MET G  34 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   TRP G  36 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'G' and resid 141 through 143
      removed outlier: 3.720A  pdb=" N   ALA G 212 " --> pdb=" O   SER G 209 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 147 through 150
      removed outlier: 3.739A  pdb=" N   GLU G 247 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY G 226 " --> pdb=" O   LEU G 246 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU G 179 " --> pdb=" O   LEU G 188 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   LEU G 188 " --> pdb=" O   LEU G 179 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1248 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2774
        1.34 -     1.46: 2142
        1.46 -     1.58: 3817
        1.58 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 8814
  Sorted by residual:
  bond pdb=" CA  TYR G 236 "
       pdb=" C   TYR G 236 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.26e-02 6.30e+03 2.07e+00
  bond pdb=" N   TYR G 236 "
       pdb=" CA  TYR G 236 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.019 1.41e-02 5.03e+03 1.81e+00
  bond pdb=" C   ACT D 401 "
       pdb=" CH3 ACT D 401 "
    ideal  model  delta    sigma   weight residual
    1.540  1.564 -0.024 2.00e-02 2.50e+03 1.42e+00
  bond pdb=" CA  PRO G 237 "
       pdb=" C   PRO G 237 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.016 1.42e-02 4.96e+03 1.21e+00
  bond pdb=" CG  ARG D 219 "
       pdb=" CD  ARG D 219 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.12e+00
  ... (remaining 8809 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.31: 11926
        4.31 -     8.62: 19
        8.62 -    12.93: 3
       12.93 -    17.24: 1
       17.24 -    21.55: 1
  Bond angle restraints: 11950
  Sorted by residual:
  angle pdb=" N   TYR G 236 "
        pdb=" CA  TYR G 236 "
        pdb=" C   TYR G 236 "
      ideal   model   delta    sigma   weight residual
     109.81  131.36  -21.55 2.21e+00 2.05e-01 9.51e+01
  angle pdb=" C   PRO G 237 "
        pdb=" CA  PRO G 237 "
        pdb=" CB  PRO G 237 "
      ideal   model   delta    sigma   weight residual
     111.56  125.26  -13.70 1.65e+00 3.67e-01 6.90e+01
  angle pdb=" C   TYR G 236 "
        pdb=" N   PRO G 237 "
        pdb=" CA  PRO G 237 "
      ideal   model   delta    sigma   weight residual
     119.84  129.57   -9.73 1.25e+00 6.40e-01 6.05e+01
  angle pdb=" N   ILE B 268 "
        pdb=" CA  ILE B 268 "
        pdb=" C   ILE B 268 "
      ideal   model   delta    sigma   weight residual
     113.71  108.76    4.95 9.50e-01 1.11e+00 2.71e+01
  angle pdb=" C   GLU G 235 "
        pdb=" N   TYR G 236 "
        pdb=" CA  TYR G 236 "
      ideal   model   delta    sigma   weight residual
     121.80  134.20  -12.40 2.44e+00 1.68e-01 2.58e+01
  ... (remaining 11945 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.06: 4629
       23.06 -    46.12: 479
       46.12 -    69.18: 82
       69.18 -    92.24: 11
       92.24 -   115.29: 1
  Dihedral angle restraints: 5202
    sinusoidal: 2003
      harmonic: 3199
  Sorted by residual:
  dihedral pdb=" CA  TYR G 236 "
           pdb=" C   TYR G 236 "
           pdb=" N   PRO G 237 "
           pdb=" CA  PRO G 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   64.71  115.29     0      5.00e+00 4.00e-02 5.32e+02
  dihedral pdb=" C   TYR G 236 "
           pdb=" N   TYR G 236 "
           pdb=" CA  TYR G 236 "
           pdb=" CB  TYR G 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -155.16   32.56     0      2.50e+00 1.60e-01 1.70e+02
  dihedral pdb=" N   TYR G 236 "
           pdb=" C   TYR G 236 "
           pdb=" CA  TYR G 236 "
           pdb=" CB  TYR G 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  155.21  -32.41     0      2.50e+00 1.60e-01 1.68e+02
  ... (remaining 5199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.299: 1351
       0.299 -    0.598: 0
       0.598 -    0.896: 1
       0.896 -    1.195: 0
       1.195 -    1.494: 1
  Chirality restraints: 1353
  Sorted by residual:
  chirality pdb=" CA  TYR G 236 "
            pdb=" N   TYR G 236 "
            pdb=" C   TYR G 236 "
            pdb=" CB  TYR G 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.02    1.49 2.00e-01 2.50e+01 5.58e+01
  chirality pdb=" CA  PRO G 237 "
            pdb=" N   PRO G 237 "
            pdb=" C   PRO G 237 "
            pdb=" CB  PRO G 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.90    0.82 2.00e-01 2.50e+01 1.69e+01
  chirality pdb=" CA  ILE G  58 "
            pdb=" N   ILE G  58 "
            pdb=" C   ILE G  58 "
            pdb=" CB  ILE G  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 1350 not shown)

  Planarity restraints: 1510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR G 236 "   -0.070 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO G 237 "    0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO G 237 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO G 237 "   -0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 162 "   -0.009 2.00e-02 2.50e+03   1.79e-02 3.19e+00
        pdb=" C   THR B 162 "    0.031 2.00e-02 2.50e+03
        pdb=" O   THR B 162 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   THR B 163 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B  59 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.65e+00
        pdb=" C   MET B  59 "    0.028 2.00e-02 2.50e+03
        pdb=" O   MET B  59 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   HIS B  60 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1507 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 165
        2.68 -     3.24: 7854
        3.24 -     3.79: 13711
        3.79 -     4.35: 18646
        4.35 -     4.90: 31245
  Nonbonded interactions: 71621
  Sorted by model distance:
  nonbonded pdb=" O   ILE D  16 "
            pdb=" OG1 THR D  20 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" O   PHE D  87 "
            pdb=" OG  SER D  91 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   MET B 323 "
            pdb=" ND2 ASN B 338 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OG  SER G 162 "
            pdb=" O   LYS G 164 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   SER G  85 "
            pdb=" OG  SER G  85 "
     model   vdw
     2.305 3.040
  ... (remaining 71616 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.01 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.090
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
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      :  0.002   0.032   8816  Z= 0.088
  Angle     :  0.551  21.547  11954  Z= 0.284
  Chirality :  0.060   1.494   1353
  Planarity :  0.004   0.106   1510
  Dihedral  : 18.152 115.295   3134
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  1.93 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 29.29 %
    Favored  : 67.60 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.09 %

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:  1.18 (0.26), residues: 1087
  helix:  1.51 (0.26), residues: 386
  sheet:  1.35 (0.32), residues: 268
  loop : -0.19 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 219 
 TYR   0.007   0.001   TYR G  59 
 PHE   0.022   0.001   PHE D 246 
 TRP   0.005   0.001   TRP B  61 
 HIS   0.001   0.000   HIS F  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 ( 8814)
  covalent geometry    : angle       0.55145 (11950)
  SS BOND              : bond        0.00134 (    2)
  SS BOND              : angle       0.44320 (    4)
  hydrogen bonds       : bond        0.24482 (  445)
  hydrogen bonds       : angle       7.40034 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 0.328 
Fit side-chains
REVERT: B  100 THR cc_start: 0.7162 (p) cc_final: 0.6654 (t)
REVERT: B  132 ARG cc_start: 0.7111 (ptp-170) cc_final: 0.6903 (ptp-170)
REVERT: C  231 ASP cc_start: 0.6889 (t0) cc_final: 0.6575 (t0)
REVERT: D   30 ARG cc_start: 0.7360 (ptm160) cc_final: 0.7134 (ptm160)
REVERT: D   56 LEU cc_start: 0.8412 (tp) cc_final: 0.8126 (tp)
REVERT: G  196 LEU cc_start: 0.8188 (mt) cc_final: 0.7969 (mm)
REVERT: G  205 SER cc_start: 0.8449 (t) cc_final: 0.8245 (p)
  outliers start: 29
  outliers final: 17
  residues processed: 247
  average time/residue: 0.5207
  time to fit residues: 137.4806
Evaluate side-chains
  231 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 214
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  203 ASP
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   65 LYS
Chi-restraints excluded: chain D residue  225 VAL
Chi-restraints excluded: chain D residue  263 SER
Chi-restraints excluded: chain D residue  275 PHE
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  185 SER
Chi-restraints excluded: chain G residue  207 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 140 HIS
B 257 GLN
C 241 ASN
C 255 ASN
C 322 HIS
G 172 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.120519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.105482 restraints weight = 12178.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.59
r_work: 0.3305 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
r_final: 0.3162
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8816  Z= 0.198
  Angle     :  0.628  10.390  11954  Z= 0.330
  Chirality :  0.047   0.342   1353
  Planarity :  0.005   0.046   1510
  Dihedral  :  6.638  59.342   1222
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.50 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 26.61 %
    Favored  : 67.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  1.37 (0.26), residues: 1087
  helix:  2.02 (0.26), residues: 394
  sheet:  0.89 (0.31), residues: 280
  loop : -0.10 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 216 
 TYR   0.016   0.002   TYR G 101 
 PHE   0.016   0.002   PHE D  89 
 TRP   0.020   0.002   TRP G  47 
 HIS   0.004   0.001   HIS D 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 8814)
  covalent geometry    : angle       0.62721 (11950)
  SS BOND              : bond        0.00796 (    2)
  SS BOND              : angle       1.27610 (    4)
  hydrogen bonds       : bond        0.04991 (  445)
  hydrogen bonds       : angle       4.97096 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 207
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8226 (p) cc_final: 0.7786 (t)
REVERT: B  132 ARG cc_start: 0.7972 (ptp-170) cc_final: 0.7704 (ptp-170)
REVERT: B  217 ARG cc_start: 0.7907 (mpt180) cc_final: 0.7672 (mpt180)
REVERT: B  232 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8021 (t80)
REVERT: B  256 ASP cc_start: 0.7586 (t0) cc_final: 0.7351 (t0)
REVERT: C   28 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7462 (mt-10)
REVERT: C   33 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7253 (mt-10)
REVERT: C  197 LYS cc_start: 0.8557 (mttm) cc_final: 0.8324 (mttm)
REVERT: C  231 ASP cc_start: 0.7180 (t0) cc_final: 0.6938 (t0)
REVERT: C  269 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7903 (p0)
REVERT: C  276 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7257 (mm-30)
REVERT: C  345 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8184 (mtpt)
REVERT: D   30 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7706 (ptm160)
REVERT: D   52 THR cc_start: 0.8608 (m) cc_final: 0.8401 (m)
REVERT: F   54 GLU cc_start: 0.7662 (pm20) cc_final: 0.7448 (pm20)
REVERT: G   18 ARG cc_start: 0.7790 (ttt180) cc_final: 0.7449 (mmt180)
REVERT: G  106 SER cc_start: 0.3073 (OUTLIER) cc_final: 0.1822 (t)
REVERT: G  228 TYR cc_start: 0.8674 (m-80) cc_final: 0.8366 (m-80)
  outliers start: 53
  outliers final: 22
  residues processed: 239
  average time/residue: 0.5600
  time to fit residues: 141.9831
Evaluate side-chains
  222 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  314 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  345 LYS
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  275 PHE
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue   71 SER
Chi-restraints excluded: chain G residue  106 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 66 optimal weight:    0.1980
   chunk 28 optimal weight:    0.7980
   chunk 91 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 228 ASN
B 291 ASN
B 338 ASN
C 255 ASN
D 248 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.118820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.104118 restraints weight = 12231.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.57
r_work: 0.3287 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       34 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8816  Z= 0.161
  Angle     :  0.562  10.215  11954  Z= 0.296
  Chirality :  0.045   0.304   1353
  Planarity :  0.004   0.038   1510
  Dihedral  :  5.860  53.200   1210
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.76 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 26.72 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  1.30 (0.25), residues: 1087
  helix:  2.14 (0.26), residues: 392
  sheet:  0.77 (0.30), residues: 276
  loop : -0.25 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 249 
 TYR   0.014   0.002   TYR G 101 
 PHE   0.012   0.002   PHE D 197 
 TRP   0.016   0.002   TRP G  47 
 HIS   0.003   0.001   HIS D 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 8814)
  covalent geometry    : angle       0.56215 (11950)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       0.80959 (    4)
  hydrogen bonds       : bond        0.04449 (  445)
  hydrogen bonds       : angle       4.71758 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 201
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8137 (p) cc_final: 0.7778 (t)
REVERT: B  140 HIS cc_start: 0.8253 (OUTLIER) cc_final: 0.7237 (m-70)
REVERT: B  232 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8043 (t80)
REVERT: B  256 ASP cc_start: 0.7574 (t0) cc_final: 0.7364 (t0)
REVERT: C   28 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7464 (mt-10)
REVERT: C  231 ASP cc_start: 0.7227 (t0) cc_final: 0.6996 (t70)
REVERT: C  255 ASN cc_start: 0.8759 (m-40) cc_final: 0.8489 (m110)
REVERT: C  276 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7296 (mm-30)
REVERT: C  317 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8040 (ttmt)
REVERT: D  127 VAL cc_start: 0.8205 (t) cc_final: 0.7751 (m)
REVERT: D  173 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6915 (mp)
REVERT: D  249 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7743 (mmm-85)
REVERT: G  106 SER cc_start: 0.3023 (OUTLIER) cc_final: 0.1797 (t)
REVERT: G  175 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8386 (tm)
REVERT: G  228 TYR cc_start: 0.8723 (m-80) cc_final: 0.8503 (m-80)
  outliers start: 48
  outliers final: 24
  residues processed: 232
  average time/residue: 0.5834
  time to fit residues: 143.6903
Evaluate side-chains
  226 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 196
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  140 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   33 GLU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  314 LYS
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue   19 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  275 PHE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  175 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 74 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 91 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 140 HIS
B 228 ASN
B 291 ASN
B 338 ASN
D 140 HIS
D 248 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.119067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.104369 restraints weight = 12389.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.60
r_work: 0.3286 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       42 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8816  Z= 0.146
  Angle     :  0.542   9.864  11954  Z= 0.285
  Chirality :  0.044   0.304   1353
  Planarity :  0.004   0.066   1510
  Dihedral  :  5.452  53.563   1204
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.68 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 27.04 %
    Favored  : 67.49 %
  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:  1.32 (0.26), residues: 1087
  helix:  2.26 (0.26), residues: 391
  sheet:  0.70 (0.29), residues: 291
  loop : -0.32 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  24 
 TYR   0.019   0.002   TYR C 320 
 PHE   0.012   0.002   PHE B 239 
 TRP   0.017   0.002   TRP B 167 
 HIS   0.003   0.001   HIS G  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 8814)
  covalent geometry    : angle       0.54176 (11950)
  SS BOND              : bond        0.00261 (    2)
  SS BOND              : angle       0.64789 (    4)
  hydrogen bonds       : bond        0.04113 (  445)
  hydrogen bonds       : angle       4.59742 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 199
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8154 (p) cc_final: 0.7817 (t)
REVERT: B  232 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8096 (t80)
REVERT: B  254 ARG cc_start: 0.7810 (mpp80) cc_final: 0.7314 (mtm180)
REVERT: B  256 ASP cc_start: 0.7566 (t0) cc_final: 0.7229 (t0)
REVERT: C   28 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7481 (mt-10)
REVERT: C  231 ASP cc_start: 0.7253 (t0) cc_final: 0.7022 (t70)
REVERT: C  255 ASN cc_start: 0.8737 (m-40) cc_final: 0.8517 (m110)
REVERT: D  127 VAL cc_start: 0.8254 (t) cc_final: 0.7828 (m)
REVERT: D  173 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6865 (mp)
REVERT: D  249 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7726 (mmm-85)
REVERT: G  106 SER cc_start: 0.2956 (OUTLIER) cc_final: 0.1783 (t)
REVERT: G  175 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8422 (tm)
REVERT: G  228 TYR cc_start: 0.8745 (m-80) cc_final: 0.8451 (m-80)
  outliers start: 51
  outliers final: 28
  residues processed: 230
  average time/residue: 0.6200
  time to fit residues: 151.2424
Evaluate side-chains
  236 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 204
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  293 SER
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue   19 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  164 CYS
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  275 PHE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain G residue   23 SER
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  116 THR
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain G residue  175 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0070
   chunk 31 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
B 228 ASN
B 291 ASN
B 338 ASN
D 140 HIS
G 172 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.120619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.105643 restraints weight = 12009.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.61
r_work: 0.3303 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3161 r_free = 0.3161    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
r_final: 0.3161
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8816  Z= 0.150
  Angle     :  0.548  10.755  11954  Z= 0.287
  Chirality :  0.044   0.248   1353
  Planarity :  0.004   0.065   1510
  Dihedral  :  5.440  56.755   1204
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.86 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 26.93 %
    Favored  : 67.27 %
  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:  1.32 (0.25), residues: 1087
  helix:  2.31 (0.26), residues: 388
  sheet:  0.62 (0.29), residues: 292
  loop : -0.29 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  24 
 TYR   0.017   0.002   TYR C 320 
 PHE   0.014   0.002   PHE D  18 
 TRP   0.016   0.002   TRP B  80 
 HIS   0.003   0.001   HIS G  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8814)
  covalent geometry    : angle       0.54806 (11950)
  SS BOND              : bond        0.00329 (    2)
  SS BOND              : angle       0.72877 (    4)
  hydrogen bonds       : bond        0.04115 (  445)
  hydrogen bonds       : angle       4.55868 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 199
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8121 (p) cc_final: 0.7801 (t)
REVERT: B  232 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8091 (t80)
REVERT: B  254 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7406 (mtm180)
REVERT: B  256 ASP cc_start: 0.7780 (t0) cc_final: 0.7430 (t0)
REVERT: C  231 ASP cc_start: 0.7264 (t0) cc_final: 0.7041 (t70)
REVERT: C  255 ASN cc_start: 0.8775 (m-40) cc_final: 0.8518 (m110)
REVERT: D   26 LEU cc_start: 0.8038 (mm) cc_final: 0.7833 (mt)
REVERT: D   52 THR cc_start: 0.8642 (m) cc_final: 0.8437 (m)
REVERT: D  127 VAL cc_start: 0.8257 (t) cc_final: 0.7806 (m)
REVERT: D  173 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6864 (mp)
REVERT: D  249 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7729 (mmm-85)
REVERT: G  106 SER cc_start: 0.2964 (OUTLIER) cc_final: 0.1753 (t)
REVERT: G  175 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8391 (tm)
REVERT: G  228 TYR cc_start: 0.8711 (m-80) cc_final: 0.8457 (m-80)
  outliers start: 54
  outliers final: 34
  residues processed: 232
  average time/residue: 0.6317
  time to fit residues: 155.2438
Evaluate side-chains
  241 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 202
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  254 ARG
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   19 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  164 CYS
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain D residue  275 PHE
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain G residue   23 SER
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  159 SER
Chi-restraints excluded: chain G residue  175 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0980
   chunk 73 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 52 optimal weight:    0.2980
   chunk 94 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
B 291 ASN
B 338 ASN
D 140 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.106753 restraints weight = 12010.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.60
r_work: 0.3323 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3188 r_free = 0.3188    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8816  Z= 0.118
  Angle     :  0.531  10.859  11954  Z= 0.276
  Chirality :  0.042   0.228   1353
  Planarity :  0.004   0.066   1510
  Dihedral  :  5.224  50.951   1204
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.40 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.47 %
    Favored  : 67.81 %
  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:  1.38 (0.26), residues: 1087
  helix:  2.34 (0.26), residues: 395
  sheet:  0.55 (0.28), residues: 302
  loop : -0.21 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 201 
 TYR   0.023   0.001   TYR G 174 
 PHE   0.012   0.001   PHE B 239 
 TRP   0.016   0.001   TRP B  80 
 HIS   0.003   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8814)
  covalent geometry    : angle       0.53065 (11950)
  SS BOND              : bond        0.00114 (    2)
  SS BOND              : angle       0.52689 (    4)
  hydrogen bonds       : bond        0.03771 (  445)
  hydrogen bonds       : angle       4.45824 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 200
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8000 (p) cc_final: 0.7717 (t)
REVERT: B  221 THR cc_start: 0.8881 (p) cc_final: 0.8396 (m)
REVERT: B  232 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8066 (t80)
REVERT: B  254 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7374 (mtm180)
REVERT: B  256 ASP cc_start: 0.7779 (t0) cc_final: 0.7443 (t0)
REVERT: C  231 ASP cc_start: 0.7237 (t0) cc_final: 0.6987 (t70)
REVERT: D   52 THR cc_start: 0.8612 (m) cc_final: 0.8405 (m)
REVERT: D  127 VAL cc_start: 0.8250 (t) cc_final: 0.7809 (m)
REVERT: D  173 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6869 (mp)
REVERT: D  249 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7694 (mmm-85)
REVERT: G  106 SER cc_start: 0.2928 (OUTLIER) cc_final: 0.1887 (t)
REVERT: G  228 TYR cc_start: 0.8707 (m-80) cc_final: 0.8398 (m-80)
  outliers start: 44
  outliers final: 26
  residues processed: 225
  average time/residue: 0.6171
  time to fit residues: 147.1968
Evaluate side-chains
  233 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 203
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  254 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  320 ASP
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  164 CYS
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  259 VAL
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  159 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    0.0670
   chunk 60 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
B 291 ASN
B 338 ASN
C 188 HIS
C 255 ASN
D 140 HIS
D 211 HIS
G 172 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.120373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105392 restraints weight = 12097.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.61
r_work: 0.3298 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8816  Z= 0.152
  Angle     :  0.548   8.099  11954  Z= 0.286
  Chirality :  0.043   0.168   1353
  Planarity :  0.004   0.052   1510
  Dihedral  :  4.955  42.699   1200
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 28.11 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1087
  helix:  2.31 (0.26), residues: 391
  sheet:  0.59 (0.29), residues: 292
  loop : -0.23 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 249 
 TYR   0.021   0.002   TYR G 174 
 PHE   0.013   0.002   PHE D  18 
 TRP   0.016   0.001   TRP B 167 
 HIS   0.016   0.001   HIS D 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8814)
  covalent geometry    : angle       0.54767 (11950)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       0.72683 (    4)
  hydrogen bonds       : bond        0.04058 (  445)
  hydrogen bonds       : angle       4.51915 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 201
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8135 (p) cc_final: 0.7844 (t)
REVERT: B  221 THR cc_start: 0.8888 (p) cc_final: 0.8399 (m)
REVERT: B  232 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8134 (t80)
REVERT: B  254 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7411 (mtm180)
REVERT: B  256 ASP cc_start: 0.7821 (t0) cc_final: 0.7502 (t0)
REVERT: C  231 ASP cc_start: 0.7269 (t0) cc_final: 0.7011 (t70)
REVERT: D  127 VAL cc_start: 0.8261 (t) cc_final: 0.7823 (m)
REVERT: D  173 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6911 (mp)
REVERT: D  187 LEU cc_start: 0.7787 (mt) cc_final: 0.7412 (mp)
REVERT: D  216 ARG cc_start: 0.7165 (mtm-85) cc_final: 0.6929 (mtm-85)
REVERT: D  249 ARG cc_start: 0.7962 (mmm-85) cc_final: 0.7711 (mmm-85)
REVERT: G   18 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7507 (mmt180)
REVERT: G  106 SER cc_start: 0.2930 (OUTLIER) cc_final: 0.1769 (t)
REVERT: G  228 TYR cc_start: 0.8714 (m-80) cc_final: 0.8442 (m-80)
  outliers start: 42
  outliers final: 29
  residues processed: 224
  average time/residue: 0.6378
  time to fit residues: 151.2507
Evaluate side-chains
  233 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 200
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  254 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  164 CYS
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain G residue   23 SER
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  159 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 106 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
B 140 HIS
B 291 ASN
B 338 ASN
D 140 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.118979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104100 restraints weight = 11865.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.58
r_work: 0.3279 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8816  Z= 0.185
  Angle     :  0.583   7.433  11954  Z= 0.305
  Chirality :  0.045   0.195   1353
  Planarity :  0.004   0.058   1510
  Dihedral  :  5.139  47.355   1200
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 27.90 %
    Favored  : 67.49 %
  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:  1.22 (0.25), residues: 1087
  helix:  2.23 (0.26), residues: 389
  sheet:  0.54 (0.29), residues: 292
  loop : -0.34 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 249 
 TYR   0.020   0.002   TYR G 174 
 PHE   0.015   0.002   PHE D  18 
 TRP   0.015   0.002   TRP B 167 
 HIS   0.003   0.001   HIS G  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 8814)
  covalent geometry    : angle       0.58265 (11950)
  SS BOND              : bond        0.00354 (    2)
  SS BOND              : angle       0.82734 (    4)
  hydrogen bonds       : bond        0.04342 (  445)
  hydrogen bonds       : angle       4.61920 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 206
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8189 (p) cc_final: 0.7842 (t)
REVERT: B  254 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7427 (mtm180)
REVERT: B  256 ASP cc_start: 0.7865 (t0) cc_final: 0.7527 (t0)
REVERT: C  231 ASP cc_start: 0.7289 (t0) cc_final: 0.7046 (t70)
REVERT: D   52 THR cc_start: 0.8633 (m) cc_final: 0.8429 (m)
REVERT: D  127 VAL cc_start: 0.8250 (t) cc_final: 0.7826 (m)
REVERT: D  173 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6925 (mp)
REVERT: D  216 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6955 (mtm-85)
REVERT: D  249 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7728 (mmm-85)
REVERT: G   18 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7515 (mmt180)
REVERT: G  106 SER cc_start: 0.2798 (OUTLIER) cc_final: 0.1548 (t)
REVERT: G  228 TYR cc_start: 0.8742 (m-80) cc_final: 0.8449 (m-80)
  outliers start: 43
  outliers final: 34
  residues processed: 229
  average time/residue: 0.6187
  time to fit residues: 150.1674
Evaluate side-chains
  239 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 202
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  254 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  164 CYS
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 SER
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  159 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 96 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0470
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
B 140 HIS
B 291 ASN
D 140 HIS
D 211 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.119926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.105073 restraints weight = 11975.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.59
r_work: 0.3295 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8816  Z= 0.155
  Angle     :  0.551   7.034  11954  Z= 0.291
  Chirality :  0.043   0.167   1353
  Planarity :  0.004   0.058   1510
  Dihedral  :  5.035  49.593   1200
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 27.25 %
    Favored  : 67.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.23 (0.25), residues: 1087
  helix:  2.25 (0.26), residues: 389
  sheet:  0.46 (0.28), residues: 299
  loop : -0.28 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 249 
 TYR   0.017   0.002   TYR G  59 
 PHE   0.012   0.002   PHE D  18 
 TRP   0.015   0.001   TRP B 167 
 HIS   0.019   0.001   HIS D 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8814)
  covalent geometry    : angle       0.55086 (11950)
  SS BOND              : bond        0.00279 (    2)
  SS BOND              : angle       0.71735 (    4)
  hydrogen bonds       : bond        0.04099 (  445)
  hydrogen bonds       : angle       4.57615 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 196
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8144 (p) cc_final: 0.7857 (t)
REVERT: B  232 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8082 (t80)
REVERT: B  254 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7388 (mtm180)
REVERT: B  256 ASP cc_start: 0.7838 (t0) cc_final: 0.7477 (t0)
REVERT: C  231 ASP cc_start: 0.7287 (t0) cc_final: 0.7052 (t70)
REVERT: D   52 THR cc_start: 0.8632 (m) cc_final: 0.8425 (m)
REVERT: D  127 VAL cc_start: 0.8251 (t) cc_final: 0.7830 (m)
REVERT: D  173 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6931 (mp)
REVERT: D  216 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6959 (mtm-85)
REVERT: D  249 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7696 (mmm-85)
REVERT: G  106 SER cc_start: 0.2738 (OUTLIER) cc_final: 0.1537 (t)
REVERT: G  228 TYR cc_start: 0.8703 (m-80) cc_final: 0.8409 (m-80)
  outliers start: 48
  outliers final: 35
  residues processed: 222
  average time/residue: 0.6035
  time to fit residues: 142.1492
Evaluate side-chains
  238 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 199
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  254 ARG
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  164 CYS
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 SER
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  159 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    0.0870
   chunk 97 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.5736

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
B 291 ASN
D 140 HIS
D 209 GLN
G  39 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.119934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.105034 restraints weight = 11914.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.59
r_work: 0.3293 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3159
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       46 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3159 r_free = 0.3159    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.3159
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8816  Z= 0.152
  Angle     :  0.558   7.708  11954  Z= 0.292
  Chirality :  0.043   0.160   1353
  Planarity :  0.004   0.061   1510
  Dihedral  :  5.010  53.742   1200
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.58 %
    Favored  : 67.49 %
  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:  1.21 (0.25), residues: 1087
  helix:  2.26 (0.26), residues: 389
  sheet:  0.47 (0.29), residues: 292
  loop : -0.33 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 249 
 TYR   0.018   0.002   TYR G  59 
 PHE   0.012   0.002   PHE D  18 
 TRP   0.015   0.001   TRP B 167 
 HIS   0.003   0.001   HIS G  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 8814)
  covalent geometry    : angle       0.55786 (11950)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       0.74451 (    4)
  hydrogen bonds       : bond        0.04079 (  445)
  hydrogen bonds       : angle       4.58618 ( 1248)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 199
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8134 (p) cc_final: 0.7861 (t)
REVERT: B  232 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8050 (t80)
REVERT: B  254 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7415 (mtm180)
REVERT: B  256 ASP cc_start: 0.7854 (t0) cc_final: 0.7519 (t0)
REVERT: C  231 ASP cc_start: 0.7285 (t0) cc_final: 0.7050 (t70)
REVERT: D   52 THR cc_start: 0.8636 (m) cc_final: 0.8431 (m)
REVERT: D  127 VAL cc_start: 0.8258 (t) cc_final: 0.7809 (m)
REVERT: D  173 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6899 (mp)
REVERT: D  187 LEU cc_start: 0.7719 (mt) cc_final: 0.7387 (mp)
REVERT: D  249 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7683 (mmm-85)
REVERT: G   18 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7442 (mmt180)
REVERT: G  106 SER cc_start: 0.2997 (OUTLIER) cc_final: 0.1798 (t)
REVERT: G  179 LEU cc_start: 0.8766 (tp) cc_final: 0.8503 (tm)
REVERT: G  228 TYR cc_start: 0.8712 (m-80) cc_final: 0.8421 (m-80)
  outliers start: 46
  outliers final: 32
  residues processed: 222
  average time/residue: 0.6285
  time to fit residues: 147.6902
Evaluate side-chains
  236 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 200
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   38 VAL
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  162 THR
Chi-restraints excluded: chain B residue  184 ASP
Chi-restraints excluded: chain B residue  185 VAL
Chi-restraints excluded: chain B residue  213 GLU
Chi-restraints excluded: chain B residue  226 ASP
Chi-restraints excluded: chain B residue  232 PHE
Chi-restraints excluded: chain B residue  254 ARG
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   49 ILE
Chi-restraints excluded: chain C residue  269 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   67 ILE
Chi-restraints excluded: chain D residue  136 MET
Chi-restraints excluded: chain D residue  164 CYS
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  250 LYS
Chi-restraints excluded: chain D residue  272 LEU
Chi-restraints excluded: chain F residue   43 GLU
Chi-restraints excluded: chain F residue   53 SER
Chi-restraints excluded: chain F residue   54 GLU
Chi-restraints excluded: chain G residue   11 LEU
Chi-restraints excluded: chain G residue   23 SER
Chi-restraints excluded: chain G residue   63 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  159 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    0.2980
   chunk 66 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
B 291 ASN
D 140 HIS
G  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.120760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.105946 restraints weight = 11924.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.59
r_work: 0.3312 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3172
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3172 r_free = 0.3172    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8816  Z= 0.131
  Angle     :  0.540   6.971  11954  Z= 0.284
  Chirality :  0.043   0.144   1353
  Planarity :  0.004   0.060   1510
  Dihedral  :  4.943  56.616   1200
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 28.11 %
    Favored  : 67.49 %
  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:  1.30 (0.26), residues: 1087
  helix:  2.32 (0.26), residues: 389
  sheet:  0.42 (0.28), residues: 309
  loop : -0.20 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 249 
 TYR   0.014   0.001   TYR G  59 
 PHE   0.012   0.001   PHE C 189 
 TRP   0.015   0.001   TRP B  80 
 HIS   0.003   0.001   HIS G  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8814)
  covalent geometry    : angle       0.53996 (11950)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.65411 (    4)
  hydrogen bonds       : bond        0.03883 (  445)
  hydrogen bonds       : angle       4.53774 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4421.76 seconds
wall clock time: 76 minutes 4.47 seconds (4564.47 seconds total)