Starting phenix.real_space_refine
on Thu Feb 13 03:19:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j24_35944/02_2025/8j24_35944.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j24_35944/02_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_35944/02_2025/8j24_35944.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j24_35944/02_2025/8j24_35944.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j24_35944/02_2025/8j24_35944.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j24_35944/02_2025/8j24_35944.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2}
          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: 5.30, per 1000 atoms: 0.61
  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: 2.20
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.92
  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: 2.54

  Time building geometry restraints manager: 2.53 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:             0.810
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.340
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.410
-------------------------------------------------------------------------------
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   8814  Z= 0.117
  Angle     :  0.551  21.547  11950  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.005   0.001   TRP B  61 
 HIS   0.001   0.000   HIS F  40 
 PHE   0.022   0.001   PHE D 246 
 TYR   0.007   0.001   TYR G  59 
 ARG   0.010   0.000   ARG D 219 

*********************** 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  : 0.908 
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: 1.1144
  time to fit residues: 295.0470
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  : 0.933 
-------------------------------------------------------------------------------
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 91 optimal weight:    0.0970
   chunk 81 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    0.1980
   chunk 32 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    8.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
B 257 GLN
C 241 ASN
C 255 ASN
C 322 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 = 0.3648 r_free = 0.3648 target = 0.122362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.107329 restraints weight = 12143.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.60
r_work: 0.3333 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3204
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3204 r_free = 0.3204    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   8814  Z= 0.237
  Angle     :  0.598  10.654  11950  Z= 0.314
  Chirality :  0.046   0.332   1353
  Planarity :  0.004   0.044   1510
  Dihedral  :  6.465  58.167   1222
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.22 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 27.79 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1087
  helix:  2.08 (0.26), residues: 394
  sheet:  0.86 (0.31), residues: 282
  loop : -0.03 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP G  47 
 HIS   0.003   0.001   HIS G  35 
 PHE   0.015   0.002   PHE D 197 
 TYR   0.013   0.002   TYR G 101 
 ARG   0.005   0.001   ARG D 216 

*********************** 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
  252 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 207
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8100 (p) cc_final: 0.7686 (t)
REVERT: B  132 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7682 (ptp-170)
REVERT: B  232 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7897 (t80)
REVERT: B  256 ASP cc_start: 0.7530 (t0) cc_final: 0.7258 (t0)
REVERT: C   20 ASP cc_start: 0.8003 (m-30) cc_final: 0.7795 (m-30)
REVERT: C   28 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7476 (mt-10)
REVERT: C  231 ASP cc_start: 0.7149 (t0) cc_final: 0.6910 (t0)
REVERT: C  276 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7320 (mm-30)
REVERT: C  345 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8196 (mtpt)
REVERT: D   30 ARG cc_start: 0.7893 (ptm160) cc_final: 0.7691 (ptm160)
REVERT: D  140 HIS cc_start: 0.8197 (m90) cc_final: 0.7995 (m-70)
REVERT: D  249 ARG cc_start: 0.7913 (mmm-85) cc_final: 0.7697 (mmm-85)
REVERT: F   54 GLU cc_start: 0.7593 (pm20) cc_final: 0.7382 (pm20)
REVERT: G   18 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7408 (mmt180)
REVERT: G  106 SER cc_start: 0.3087 (OUTLIER) cc_final: 0.1911 (t)
  outliers start: 45
  outliers final: 18
  residues processed: 234
  average time/residue: 1.2123
  time to fit residues: 302.2656
Evaluate side-chains
  216 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 195
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 THR
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  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  314 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  345 LYS
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  106 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 104 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 248 GLN
G 172 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.118107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.103255 restraints weight = 12260.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.58
r_work: 0.3260 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3127
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8814  Z= 0.324
  Angle     :  0.599  10.198  11950  Z= 0.315
  Chirality :  0.046   0.323   1353
  Planarity :  0.004   0.039   1510
  Dihedral  :  5.939  54.338   1207
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.31 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 26.82 %
    Favored  : 67.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.25), residues: 1087
  helix:  2.06 (0.26), residues: 392
  sheet:  0.74 (0.30), residues: 289
  loop : -0.30 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP G  47 
 HIS   0.005   0.001   HIS D 140 
 PHE   0.026   0.002   PHE D 246 
 TYR   0.016   0.002   TYR G 101 
 ARG   0.006   0.001   ARG B 249 

*********************** 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
  247 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 198
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8302 (p) cc_final: 0.7880 (t)
REVERT: B  132 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7727 (ptp-170)
REVERT: B  232 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8017 (t80)
REVERT: C   28 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7456 (mt-10)
REVERT: C  231 ASP cc_start: 0.7283 (t0) cc_final: 0.7031 (t70)
REVERT: D   65 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.6615 (mptt)
REVERT: D  127 VAL cc_start: 0.8209 (t) cc_final: 0.7779 (m)
REVERT: D  173 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7018 (mp)
REVERT: G  106 SER cc_start: 0.3010 (OUTLIER) cc_final: 0.1845 (t)
  outliers start: 49
  outliers final: 26
  residues processed: 230
  average time/residue: 1.2253
  time to fit residues: 299.5381
Evaluate side-chains
  230 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 200
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  314 LYS
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue   19 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   65 LYS
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9990
   chunk 70 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9990
   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 = 0.3591 r_free = 0.3591 target = 0.118149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.103629 restraints weight = 12247.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.58
r_work: 0.3267 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3134 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       38 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8814  Z= 0.245
  Angle     :  0.550   9.807  11950  Z= 0.292
  Chirality :  0.044   0.312   1353
  Planarity :  0.004   0.064   1510
  Dihedral  :  5.728  54.502   1206
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.40 %
    Favored  : 96.50 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.25), residues: 1087
  helix:  2.23 (0.26), residues: 386
  sheet:  0.62 (0.30), residues: 283
  loop : -0.32 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  80 
 HIS   0.003   0.001   HIS G  35 
 PHE   0.015   0.002   PHE D 246 
 TYR   0.021   0.002   TYR C 320 
 ARG   0.006   0.000   ARG C  24 

*********************** 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
  258 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 204
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8192 (p) cc_final: 0.7829 (t)
REVERT: B  232 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8024 (t80)
REVERT: B  254 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7348 (mtm180)
REVERT: C   28 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7462 (mt-10)
REVERT: C  231 ASP cc_start: 0.7283 (t0) cc_final: 0.7029 (t70)
REVERT: C  255 ASN cc_start: 0.8711 (m-40) cc_final: 0.8461 (m110)
REVERT: C  345 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8154 (mppt)
REVERT: D   52 THR cc_start: 0.8611 (m) cc_final: 0.8408 (m)
REVERT: D  127 VAL cc_start: 0.8256 (t) cc_final: 0.7824 (m)
REVERT: D  173 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6961 (mp)
REVERT: G  106 SER cc_start: 0.2949 (OUTLIER) cc_final: 0.1735 (t)
REVERT: G  175 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8380 (tm)
REVERT: G  228 TYR cc_start: 0.8747 (m-80) cc_final: 0.8408 (m-80)
  outliers start: 54
  outliers final: 26
  residues processed: 236
  average time/residue: 1.2145
  time to fit residues: 304.8368
Evaluate side-chains
  233 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 201
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
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  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  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  275 GLU
Chi-restraints excluded: chain C residue  293 SER
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  345 LYS
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  226 VAL
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   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  175 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3603 r_free = 0.3603 target = 0.119371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.104490 restraints weight = 11951.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.59
r_work: 0.3267 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       45 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8814  Z= 0.290
  Angle     :  0.574  10.941  11950  Z= 0.303
  Chirality :  0.045   0.260   1353
  Planarity :  0.004   0.065   1510
  Dihedral  :  5.616  56.981   1204
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.86 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 26.50 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1087
  helix:  2.13 (0.26), residues: 389
  sheet:  0.54 (0.29), residues: 292
  loop : -0.33 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 167 
 HIS   0.003   0.001   HIS F  40 
 PHE   0.015   0.002   PHE D  18 
 TYR   0.023   0.002   TYR C 320 
 ARG   0.005   0.000   ARG D 201 

*********************** 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
  254 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 201
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7957 (mtt180)
REVERT: B  100 THR cc_start: 0.8200 (p) cc_final: 0.7849 (t)
REVERT: B  254 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7435 (mtm180)
REVERT: C  231 ASP cc_start: 0.7291 (t0) cc_final: 0.7056 (t70)
REVERT: C  255 ASN cc_start: 0.8810 (m-40) cc_final: 0.8530 (m110)
REVERT: C  345 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8233 (mppt)
REVERT: D   65 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.6840 (mptt)
REVERT: D  127 VAL cc_start: 0.8251 (t) cc_final: 0.7824 (m)
REVERT: D  173 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7000 (mp)
REVERT: D  249 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7734 (mmm-85)
REVERT: G  106 SER cc_start: 0.3044 (OUTLIER) cc_final: 0.1826 (t)
REVERT: G  228 TYR cc_start: 0.8746 (m-80) cc_final: 0.8527 (m-80)
  outliers start: 53
  outliers final: 35
  residues processed: 233
  average time/residue: 1.2818
  time to fit residues: 316.8277
Evaluate side-chains
  242 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 202
  time to evaluate  : 1.588 
-------------------------------------------------------------------------------
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  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  324 THR
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  345 LYS
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   65 LYS
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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
D 211 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.118415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.103578 restraints weight = 11884.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.57
r_work: 0.3252 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8814  Z= 0.335
  Angle     :  0.595   8.607  11950  Z= 0.314
  Chirality :  0.046   0.229   1353
  Planarity :  0.004   0.051   1510
  Dihedral  :  5.657  56.201   1204
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 26.07 %
    Favored  : 68.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.26), residues: 1087
  helix:  2.16 (0.26), residues: 385
  sheet:  0.44 (0.29), residues: 302
  loop : -0.34 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 167 
 HIS   0.014   0.001   HIS D 211 
 PHE   0.015   0.002   PHE D  18 
 TYR   0.023   0.002   TYR G 236 
 ARG   0.005   0.000   ARG B 249 

*********************** 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
  255 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 200
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8220 (p) cc_final: 0.7842 (t)
REVERT: B  221 THR cc_start: 0.8902 (p) cc_final: 0.8399 (m)
REVERT: B  254 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7450 (mtm180)
REVERT: C  231 ASP cc_start: 0.7342 (t0) cc_final: 0.7094 (t70)
REVERT: C  255 ASN cc_start: 0.8851 (m-40) cc_final: 0.8591 (m110)
REVERT: C  345 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8346 (mtpt)
REVERT: D   65 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.6841 (mptt)
REVERT: D  127 VAL cc_start: 0.8247 (t) cc_final: 0.7820 (m)
REVERT: D  173 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7048 (mp)
REVERT: D  249 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7694 (mmm-85)
REVERT: G  106 SER cc_start: 0.3006 (OUTLIER) cc_final: 0.1780 (t)
REVERT: G  228 TYR cc_start: 0.8770 (m-80) cc_final: 0.8473 (m-80)
  outliers start: 55
  outliers final: 36
  residues processed: 232
  average time/residue: 1.2634
  time to fit residues: 311.3875
Evaluate side-chains
  238 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 197
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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  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  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 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 C residue  345 LYS
Chi-restraints excluded: chain D residue    9 LEU
Chi-restraints excluded: chain D residue   12 MET
Chi-restraints excluded: chain D residue   19 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   65 LYS
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  226 VAL
Chi-restraints excluded: chain D residue  250 LYS
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0070
   chunk 12 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
B 228 ASN
B 235 ASN
B 237 ASN
B 291 ASN
B 338 ASN
D 140 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.119326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.104498 restraints weight = 11950.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 1.59
r_work: 0.3285 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       48 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8814  Z= 0.248
  Angle     :  0.554   7.367  11950  Z= 0.294
  Chirality :  0.044   0.190   1353
  Planarity :  0.004   0.057   1510
  Dihedral  :  5.432  52.109   1204
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 26.18 %
    Favored  : 68.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.26), residues: 1087
  helix:  2.26 (0.26), residues: 385
  sheet:  0.51 (0.29), residues: 292
  loop : -0.38 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  80 
 HIS   0.003   0.001   HIS B  89 
 PHE   0.012   0.002   PHE B 239 
 TYR   0.018   0.002   TYR G 236 
 ARG   0.005   0.000   ARG C  24 

*********************** 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
  249 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 197
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: B   42 GLN cc_start: 0.8494 (mt0) cc_final: 0.8284 (mm-40)
REVERT: B  100 THR cc_start: 0.8152 (p) cc_final: 0.7859 (t)
REVERT: B  221 THR cc_start: 0.8892 (p) cc_final: 0.8398 (m)
REVERT: B  232 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8035 (t80)
REVERT: B  254 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7439 (mtm180)
REVERT: C  231 ASP cc_start: 0.7302 (t0) cc_final: 0.7062 (t70)
REVERT: C  255 ASN cc_start: 0.8782 (m-40) cc_final: 0.8530 (m110)
REVERT: D  127 VAL cc_start: 0.8249 (t) cc_final: 0.7832 (m)
REVERT: D  173 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7058 (mp)
REVERT: D  249 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7706 (mmm-85)
REVERT: G   57 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8231 (m)
REVERT: G  106 SER cc_start: 0.2850 (OUTLIER) cc_final: 0.1663 (t)
REVERT: G  228 TYR cc_start: 0.8696 (m-80) cc_final: 0.8434 (m-80)
  outliers start: 52
  outliers final: 38
  residues processed: 228
  average time/residue: 1.2333
  time to fit residues: 298.9328
Evaluate side-chains
  239 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 196
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   99 MET
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  155 ILE
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  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   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  143 ILE
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   23 SER
Chi-restraints excluded: chain G residue   57 THR
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 35 optimal weight:    0.6980
   chunk 103 optimal weight:    0.0010
   chunk 69 optimal weight:    3.9990
   chunk 101 optimal weight:    0.2980
   chunk 99 optimal weight:    0.2980
   chunk 90 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0070
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.2604

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

Flipped N/Q/H residues before XYZ refinement:
B 235 ASN
B 257 GLN
B 291 ASN
B 338 ASN
D 140 HIS
D 211 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.121636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.106834 restraints weight = 12063.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.60
r_work: 0.3317 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3188
|-occupancy refinement: start-------------------------------------------------|
| 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:       48 |
|-----------------------------------------------------------------------------|
|-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:       50 |
|-----------------------------------------------------------------------------|
r_final: 0.3188
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8814  Z= 0.154
  Angle     :  0.516   7.146  11950  Z= 0.272
  Chirality :  0.042   0.147   1353
  Planarity :  0.004   0.058   1510
  Dihedral  :  5.058  48.744   1202
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 27.04 %
    Favored  : 68.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.26), residues: 1087
  helix:  2.40 (0.26), residues: 391
  sheet:  0.42 (0.29), residues: 289
  loop : -0.24 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  80 
 HIS   0.012   0.001   HIS D 211 
 PHE   0.011   0.001   PHE B 239 
 TYR   0.015   0.001   TYR G 191 
 ARG   0.004   0.000   ARG B 249 

*********************** 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
  246 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 204
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.7924 (p) cc_final: 0.7706 (t)
REVERT: B  221 THR cc_start: 0.8903 (p) cc_final: 0.8415 (m)
REVERT: B  232 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7986 (t80)
REVERT: B  254 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7441 (mtm180)
REVERT: C  231 ASP cc_start: 0.7238 (t0) cc_final: 0.6994 (t70)
REVERT: C  255 ASN cc_start: 0.8552 (m-40) cc_final: 0.8239 (m-40)
REVERT: D  127 VAL cc_start: 0.8247 (t) cc_final: 0.7796 (m)
REVERT: D  249 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7713 (mmm-85)
REVERT: G   18 ARG cc_start: 0.7909 (ttt180) cc_final: 0.7462 (mmt180)
REVERT: G  106 SER cc_start: 0.2772 (OUTLIER) cc_final: 0.1747 (m)
REVERT: G  228 TYR cc_start: 0.8686 (m-80) cc_final: 0.8422 (m-80)
  outliers start: 42
  outliers final: 22
  residues processed: 229
  average time/residue: 1.3073
  time to fit residues: 317.5213
Evaluate side-chains
  225 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 200
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   63 THR
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  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 F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
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 45 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0370
   chunk 70 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
B 235 ASN
B 291 ASN
B 338 ASN
D 140 HIS
D 209 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.120746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.105935 restraints weight = 11920.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.59
r_work: 0.3301 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.3240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8814  Z= 0.205
  Angle     :  0.543   6.895  11950  Z= 0.286
  Chirality :  0.043   0.191   1353
  Planarity :  0.004   0.061   1510
  Dihedral  :  4.928  50.329   1200
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 27.68 %
    Favored  : 68.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.26), residues: 1087
  helix:  2.41 (0.26), residues: 387
  sheet:  0.48 (0.29), residues: 292
  loop : -0.28 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  80 
 HIS   0.002   0.001   HIS G  35 
 PHE   0.012   0.001   PHE D  18 
 TYR   0.014   0.001   TYR G  59 
 ARG   0.004   0.000   ARG B 249 

*********************** 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
  233 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 198
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.7995 (p) cc_final: 0.7777 (t)
REVERT: B  221 THR cc_start: 0.8900 (p) cc_final: 0.8400 (m)
REVERT: B  232 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8138 (t80)
REVERT: B  254 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7447 (mtm180)
REVERT: C  231 ASP cc_start: 0.7270 (t0) cc_final: 0.7030 (t70)
REVERT: C  255 ASN cc_start: 0.8546 (m-40) cc_final: 0.8238 (m-40)
REVERT: D  127 VAL cc_start: 0.8259 (t) cc_final: 0.7790 (m)
REVERT: G   18 ARG cc_start: 0.7929 (ttt180) cc_final: 0.7489 (mmt180)
REVERT: G  106 SER cc_start: 0.2875 (OUTLIER) cc_final: 0.1751 (t)
REVERT: G  228 TYR cc_start: 0.8683 (m-80) cc_final: 0.8442 (m-80)
  outliers start: 35
  outliers final: 20
  residues processed: 219
  average time/residue: 1.3130
  time to fit residues: 304.8066
Evaluate side-chains
  216 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 193
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
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   63 THR
Chi-restraints excluded: chain B residue   99 MET
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 C residue  269 ASN
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
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 F residue   43 GLU
Chi-restraints excluded: chain F residue   54 GLU
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 4 optimal weight:    0.8980
   chunk 98 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 102 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 78 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  73 GLN
B 237 ASN
B 291 ASN
B 338 ASN
D 140 HIS
D 209 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.120115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.105297 restraints weight = 11934.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.58
r_work: 0.3294 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8814  Z= 0.237
  Angle     :  0.566   7.794  11950  Z= 0.297
  Chirality :  0.044   0.190   1353
  Planarity :  0.004   0.060   1510
  Dihedral  :  5.030  53.063   1200
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 28.65 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1087
  helix:  2.34 (0.26), residues: 388
  sheet:  0.48 (0.29), residues: 292
  loop : -0.30 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  80 
 HIS   0.003   0.001   HIS G  35 
 PHE   0.013   0.002   PHE D  18 
 TYR   0.017   0.002   TYR G 174 
 ARG   0.004   0.000   ARG B 249 

********************** 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
  227 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 194
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: B  100 THR cc_start: 0.8122 (p) cc_final: 0.7835 (t)
REVERT: B  221 THR cc_start: 0.8890 (p) cc_final: 0.8400 (m)
REVERT: B  232 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8104 (t80)
REVERT: B  254 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7452 (mtm180)
REVERT: C  231 ASP cc_start: 0.7304 (t0) cc_final: 0.7078 (t70)
REVERT: C  255 ASN cc_start: 0.8586 (m-40) cc_final: 0.8269 (m-40)
REVERT: C  317 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7718 (ttpt)
REVERT: D  127 VAL cc_start: 0.8269 (t) cc_final: 0.7836 (m)
REVERT: D  173 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6919 (mp)
REVERT: D  187 LEU cc_start: 0.7683 (mt) cc_final: 0.7397 (mp)
REVERT: G   18 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7539 (mmt180)
REVERT: G   57 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8200 (m)
REVERT: G  106 SER cc_start: 0.2861 (OUTLIER) cc_final: 0.1763 (t)
REVERT: G  228 TYR cc_start: 0.8719 (m-80) cc_final: 0.8418 (m-80)
  outliers start: 33
  outliers final: 23
  residues processed: 213
  average time/residue: 1.3451
  time to fit residues: 303.7625
Evaluate side-chains
  221 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 192
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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   63 THR
Chi-restraints excluded: chain B residue   99 MET
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 C residue  269 ASN
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  317 LYS
Chi-restraints excluded: chain C residue  330 LYS
Chi-restraints excluded: chain C residue  332 VAL
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   57 THR
Chi-restraints excluded: chain G residue  106 SER
Chi-restraints excluded: chain G residue  156 VAL
Chi-restraints excluded: chain G residue  175 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0970
   chunk 92 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 88 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 84 optimal weight:    0.4980
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
B 235 ASN
B 237 ASN
B 291 ASN
D 140 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.121146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.106309 restraints weight = 12047.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.59
r_work: 0.3312 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
|-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:       53 |
|-----------------------------------------------------------------------------|
r_final: 0.3172
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8814  Z= 0.188
  Angle     :  0.540   6.753  11950  Z= 0.285
  Chirality :  0.042   0.171   1353
  Planarity :  0.004   0.059   1510
  Dihedral  :  4.935  56.540   1200
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 28.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.26), residues: 1087
  helix:  2.41 (0.26), residues: 388
  sheet:  0.40 (0.30), residues: 279
  loop : -0.25 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  80 
 HIS   0.003   0.001   HIS D 211 
 PHE   0.012   0.001   PHE D  18 
 TYR   0.015   0.001   TYR G  59 
 ARG   0.005   0.000   ARG B 249 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8341.62 seconds
wall clock time: 147 minutes 29.86 seconds (8849.86 seconds total)