Starting phenix.real_space_refine
on Wed Jan 15 23:57:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xzi_38797/01_2025/8xzi_38797_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xzi_38797/01_2025/8xzi_38797.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xzi_38797/01_2025/8xzi_38797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xzi_38797/01_2025/8xzi_38797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xzi_38797/01_2025/8xzi_38797_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xzi_38797/01_2025/8xzi_38797_trim.cif"
  }
  resolution = 2.7
  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=   0.002 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      73      5.16       5
     C    5758      2.51       5
     N    1528      2.21       5
     O    1682      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9041
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2473
          Classifications: {'peptide': 309}
          Link IDs: {'PTRANS': 11, 'TRANS': 297}
    Chain: "A"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1756
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2553
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 327}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'A1D5N': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.62, per 1000 atoms: 0.62
  Number of scatterers: 9041
  At special positions: 0
  Unit cell: (101.352, 131.016, 115.36, 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      73     16.00
     O    1682      8.00
     N    1528      7.00
     C    5758      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 281 " distance=2.08
    Simple disulfide: pdb=" SG  CYS R 102 " - pdb=" SG  CYS R 181 " distance=2.12
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.02

  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: 2.12
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 16 sheets defined
      40.7% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'R' and resid 26 through 56
      Proline residue:  R  32  - end of helix
    Processing helix  chain 'R' and resid 64 through 81
      removed outlier: 4.170A  pdb=" N   THR R  81 " --> pdb=" O   THR R  77 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 81 through 91
      removed outlier: 4.095A  pdb=" N   TRP R  85 " --> pdb=" O   THR R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 98 through 132
      removed outlier: 3.535A  pdb=" N   VAL R 117 " --> pdb=" O   MET R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.058A  pdb=" N   ARG R 143 " --> pdb=" O   ARG R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 161
    Processing helix  chain 'R' and resid 161 through 167
      removed outlier: 3.707A  pdb=" N   MET R 165 " --> pdb=" O   ALA R 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 193
      No H-bonds generated for 'chain 'R' and resid 191 through 193'
    Processing helix  chain 'R' and resid 194 through 210
    Processing helix  chain 'R' and resid 210 through 232
    Processing helix  chain 'R' and resid 237 through 277
      Proline residue:  R 263  - end of helix
      removed outlier: 3.548A  pdb=" N   SER R 275 " --> pdb=" O   TYR R 271 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU R 276 " --> pdb=" O   MET R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 299
      Proline residue:  R 292  - end of helix
    Processing helix  chain 'R' and resid 299 through 310
      removed outlier: 3.640A  pdb=" N   CYS R 303 " --> pdb=" O   TYR R 299 " (cutoff:3.500A)
      Proline residue:  R 306  - end of helix
    Processing helix  chain 'R' and resid 313 through 325
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.907A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.525A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.799A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'G' and resid 6 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.139A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 74 through 77
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 208 through 212
    Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.602A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 9.150A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.442A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.256A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.737A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.867A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.157A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.611A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.926A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.627A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.515A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 5
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.715A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 4.338A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 18 through 19
    Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136
      removed outlier: 4.752A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 6.300A  pdb=" N   ASN S 182 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.540A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)

    488 hydrogen bonds defined for protein.
    1332 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: 2.44 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1510
        1.30 -     1.43: 2567
        1.43 -     1.56: 5024
        1.56 -     1.69: 35
        1.69 -     1.82: 101
  Bond restraints: 9237
  Sorted by residual:
  bond pdb=" C28 A1D5N R 401 "
       pdb=" S01 A1D5N R 401 "
    ideal  model  delta    sigma   weight residual
    1.722  1.545  0.177 2.00e-02 2.50e+03 7.84e+01
  bond pdb=" C16 A1D5N R 401 "
       pdb=" C21 A1D5N R 401 "
    ideal  model  delta    sigma   weight residual
    1.389  1.566 -0.177 2.00e-02 2.50e+03 7.81e+01
  bond pdb=" C11 A1D5N R 401 "
       pdb=" C18 A1D5N R 401 "
    ideal  model  delta    sigma   weight residual
    1.393  1.565 -0.172 2.00e-02 2.50e+03 7.36e+01
  bond pdb=" C30 A1D5N R 401 "
       pdb=" C31 A1D5N R 401 "
    ideal  model  delta    sigma   weight residual
    1.422  1.593 -0.171 2.00e-02 2.50e+03 7.33e+01
  bond pdb=" C32 A1D5N R 401 "
       pdb=" S01 A1D5N R 401 "
    ideal  model  delta    sigma   weight residual
    1.714  1.551  0.163 2.00e-02 2.50e+03 6.63e+01
  ... (remaining 9232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 11561
        3.09 -     6.19: 880
        6.19 -     9.28: 61
        9.28 -    12.37: 4
       12.37 -    15.47: 5
  Bond angle restraints: 12511
  Sorted by residual:
  angle pdb=" N   ARG R  91 "
        pdb=" CA  ARG R  91 "
        pdb=" C   ARG R  91 "
      ideal   model   delta    sigma   weight residual
     110.53   97.92   12.61 1.32e+00 5.74e-01 9.12e+01
  angle pdb=" C   SER S 106 "
        pdb=" N   PRO S 107 "
        pdb=" CA  PRO S 107 "
      ideal   model   delta    sigma   weight residual
     119.78  128.74   -8.96 1.03e+00 9.43e-01 7.56e+01
  angle pdb=" N   ARG S 179 "
        pdb=" CA  ARG S 179 "
        pdb=" C   ARG S 179 "
      ideal   model   delta    sigma   weight residual
     110.14   96.83   13.31 1.55e+00 4.16e-01 7.37e+01
  angle pdb=" C   ASP G  48 "
        pdb=" N   PRO G  49 "
        pdb=" CA  PRO G  49 "
      ideal   model   delta    sigma   weight residual
     119.56  128.03   -8.47 1.02e+00 9.61e-01 6.89e+01
  angle pdb=" CA  PHE B 199 "
        pdb=" CB  PHE B 199 "
        pdb=" CG  PHE B 199 "
      ideal   model   delta    sigma   weight residual
     113.80  121.86   -8.06 1.00e+00 1.00e+00 6.50e+01
  ... (remaining 12506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 5304
       17.23 -    34.46: 131
       34.46 -    51.69: 17
       51.69 -    68.92: 14
       68.92 -    86.14: 4
  Dihedral angle restraints: 5470
    sinusoidal: 2137
      harmonic: 3333
  Sorted by residual:
  dihedral pdb=" C   PHE B 241 "
           pdb=" N   PHE B 241 "
           pdb=" CA  PHE B 241 "
           pdb=" CB  PHE B 241 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.76  -15.84     0      2.50e+00 1.60e-01 4.01e+01
  dihedral pdb=" C   PHE B 199 "
           pdb=" N   PHE B 199 "
           pdb=" CA  PHE B 199 "
           pdb=" CB  PHE B 199 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.20  -15.40     0      2.50e+00 1.60e-01 3.79e+01
  dihedral pdb=" C   TRP B  82 "
           pdb=" N   TRP B  82 "
           pdb=" CA  TRP B  82 "
           pdb=" CB  TRP B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -114.04   -8.56     0      2.50e+00 1.60e-01 1.17e+01
  ... (remaining 5467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 899
       0.081 -    0.161: 395
       0.161 -    0.242: 88
       0.242 -    0.322: 25
       0.322 -    0.403: 1
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CA  ASN R 112 "
            pdb=" N   ASN R 112 "
            pdb=" C   ASN R 112 "
            pdb=" CB  ASN R 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CA  TYR R 221 "
            pdb=" N   TYR R 221 "
            pdb=" C   TYR R 221 "
            pdb=" CB  TYR R 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CB  THR R 170 "
            pdb=" CA  THR R 170 "
            pdb=" OG1 THR R 170 "
            pdb=" CG2 THR R 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.23    0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.059 2.00e-02 2.50e+03   3.00e-02 1.80e+01
        pdb=" CG  TYR B 105 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S  50 "   -0.053 2.00e-02 2.50e+03   2.80e-02 1.57e+01
        pdb=" CG  TYR S  50 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR S  50 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR S  50 "    0.028 2.00e-02 2.50e+03
        pdb=" CE1 TYR S  50 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR S  50 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR S  50 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR S  50 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G  40 "    0.048 2.00e-02 2.50e+03   2.69e-02 1.45e+01
        pdb=" CG  TYR G  40 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR G  40 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR G  40 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR G  40 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR G  40 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR G  40 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR G  40 "    0.044 2.00e-02 2.50e+03
  ... (remaining 1570 not shown)

  Histogram of nonbonded interaction distances:
        1.23 -     1.96: 1
        1.96 -     2.70: 544
        2.70 -     3.43: 12384
        3.43 -     4.17: 23553
        4.17 -     4.90: 40949
  Nonbonded interactions: 77431
  Sorted by model distance:
  nonbonded pdb=" O   ASP R  23 "
            pdb=" N   LYS R  25 "
     model   vdw
     1.226 3.120
  nonbonded pdb=" C   ASP R  23 "
            pdb=" N   LYS R  25 "
     model   vdw
     2.118 3.350
  nonbonded pdb=" O   ASP R  23 "
            pdb=" CA  LYS R  25 "
     model   vdw
     2.126 3.470
  nonbonded pdb=" O   ASP R  23 "
            pdb=" C   TRP R  24 "
     model   vdw
     2.300 3.270
  nonbonded pdb=" N   ARG S 179 "
            pdb=" O   ARG S 179 "
     model   vdw
     2.313 2.496
  ... (remaining 77426 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=1.00 max=1.00 mean=1.00
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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     22.600
  Find NCS groups from input model:        0.100
  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:12.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
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      :  0.021   0.181   9237  Z= 1.329
  Angle     :  1.723  15.465  12511  Z= 1.156
  Chirality :  0.093   0.403   1408
  Planarity :  0.009   0.041   1573
  Dihedral  :  9.398  86.144   3310
  Min Nonbonded Distance : 1.226

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  2.21 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.41 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.22 (0.25), residues: 1131
  helix:  0.55 (0.24), residues: 400
  sheet:  1.25 (0.31), residues: 268
  loop :  1.03 (0.31), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.009   TRP B  99 
 HIS   0.011   0.003   HIS A 213 
 PHE   0.039   0.006   PHE A 199 
 TYR   0.059   0.007   TYR B 105 
 ARG   0.013   0.001   ARG S  98 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: R   62 ARG cc_start: 0.6894 (ptt180) cc_final: 0.6639 (mtt90)
REVERT: R  271 TYR cc_start: 0.8235 (t80) cc_final: 0.7953 (t80)
REVERT: A  195 HIS cc_start: 0.7655 (t70) cc_final: 0.7423 (t70)
REVERT: A  271 LYS cc_start: 0.6732 (pttp) cc_final: 0.6530 (pttp)
REVERT: B  129 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7513 (mmm-85)
REVERT: B  199 PHE cc_start: 0.5958 (m-10) cc_final: 0.5608 (m-80)
REVERT: S   23 SER cc_start: 0.8188 (t) cc_final: 0.7984 (m)
REVERT: S   77 ASN cc_start: 0.8283 (m-40) cc_final: 0.8044 (m110)
REVERT: S  113 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7729 (mm110)
REVERT: S  207 LEU cc_start: 0.7344 (tp) cc_final: 0.6691 (tt)
REVERT: S  212 VAL cc_start: 0.8049 (p) cc_final: 0.7722 (t)
  outliers start: 2
  outliers final: 1
  residues processed: 210
  average time/residue: 1.4948
  time to fit residues: 331.3180
Evaluate side-chains
  144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 28 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    0.4980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.132160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.105610 restraints weight = 12643.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.98
r_work: 0.3217 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9237  Z= 0.221
  Angle     :  0.650   9.250  12511  Z= 0.353
  Chirality :  0.045   0.174   1408
  Planarity :  0.004   0.038   1573
  Dihedral  :  5.586  37.780   1277
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.03 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.34 %
    Favored  : 89.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.54 (0.25), residues: 1131
  helix:  1.70 (0.25), residues: 414
  sheet:  1.25 (0.31), residues: 258
  loop :  0.37 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP R  51 
 HIS   0.005   0.001   HIS G  44 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.015   0.002   TYR S  59 
 ARG   0.008   0.001   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 1.054 
Fit side-chains
REVERT: R   30 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8225 (mt)
REVERT: R   62 ARG cc_start: 0.7378 (ptt180) cc_final: 0.6833 (mtt90)
REVERT: R  170 THR cc_start: 0.7196 (OUTLIER) cc_final: 0.6928 (p)
REVERT: R  204 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8222 (m)
REVERT: R  271 TYR cc_start: 0.8695 (t80) cc_final: 0.8376 (t80)
REVERT: R  285 LEU cc_start: 0.8098 (mt) cc_final: 0.7893 (mm)
REVERT: A   24 ARG cc_start: 0.7801 (ttp-110) cc_final: 0.7421 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7282 (tt0)
REVERT: A  186 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7522 (mt-10)
REVERT: B  325 MET cc_start: 0.8512 (mmm) cc_final: 0.7939 (tpp)
REVERT: S  132 THR cc_start: 0.7214 (m) cc_final: 0.6993 (t)
REVERT: S  207 LEU cc_start: 0.7875 (tp) cc_final: 0.7637 (tt)
  outliers start: 17
  outliers final: 4
  residues processed: 169
  average time/residue: 1.4599
  time to fit residues: 261.1696
Evaluate side-chains
  145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 137
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   30 LEU
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  277 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 103 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 72 optimal weight:    9.9990
   chunk 89 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 64 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   overall best weight:    1.3984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.130476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103919 restraints weight = 12752.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.95
r_work: 0.3194 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9237  Z= 0.227
  Angle     :  0.608   8.110  12511  Z= 0.327
  Chirality :  0.044   0.169   1408
  Planarity :  0.004   0.042   1573
  Dihedral  :  5.324  42.984   1275
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.87 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.41 (0.25), residues: 1131
  helix:  1.80 (0.25), residues: 421
  sheet:  1.02 (0.31), residues: 261
  loop :  0.15 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R  51 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.014   0.002   TYR R  88 
 ARG   0.009   0.001   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.938 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7236 (ptt180) cc_final: 0.6789 (mpt180)
REVERT: R  204 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8198 (m)
REVERT: R  285 LEU cc_start: 0.8132 (mt) cc_final: 0.7895 (mm)
REVERT: A   24 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7409 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7015 (tt0)
REVERT: A  186 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7495 (mt-10)
REVERT: A  192 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7225 (mptt)
REVERT: A  209 LYS cc_start: 0.8257 (ptmm) cc_final: 0.7722 (mmmt)
REVERT: G   58 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7281 (tp30)
REVERT: S  207 LEU cc_start: 0.7976 (tp) cc_final: 0.7766 (tt)
  outliers start: 21
  outliers final: 7
  residues processed: 154
  average time/residue: 1.5500
  time to fit residues: 251.6249
Evaluate side-chains
  142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  192 LYS
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 102 optimal weight:    0.5980
   chunk 109 optimal weight:    6.9990
   chunk 57 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.130435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.104099 restraints weight = 12654.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.96
r_work: 0.3196 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9237  Z= 0.199
  Angle     :  0.574   9.514  12511  Z= 0.307
  Chirality :  0.043   0.170   1408
  Planarity :  0.004   0.043   1573
  Dihedral  :  5.137  41.563   1275
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 10.07 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.41 (0.25), residues: 1131
  helix:  1.90 (0.26), residues: 420
  sheet:  0.87 (0.31), residues: 263
  loop :  0.14 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R  51 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.016   0.002   PHE B 151 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.010   0.000   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.936 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7268 (ptt180) cc_final: 0.6872 (mpt180)
REVERT: R  204 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8196 (m)
REVERT: R  271 TYR cc_start: 0.8704 (t80) cc_final: 0.8399 (t80)
REVERT: R  285 LEU cc_start: 0.8160 (mt) cc_final: 0.7920 (mm)
REVERT: A   24 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7384 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7059 (tt0)
REVERT: A  192 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7171 (mptt)
REVERT: B   42 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6900 (tpp-160)
REVERT: B  226 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7747 (mm-30)
REVERT: G   58 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7241 (tp30)
REVERT: S   76 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7509 (mptt)
REVERT: S  207 LEU cc_start: 0.7980 (tp) cc_final: 0.7776 (tt)
  outliers start: 24
  outliers final: 8
  residues processed: 152
  average time/residue: 1.5120
  time to fit residues: 242.8313
Evaluate side-chains
  146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   40 LEU
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  192 LYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:   10.0000
   chunk 67 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 43 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   overall best weight:    2.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.103951 restraints weight = 12635.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.97
r_work: 0.3158 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9237  Z= 0.292
  Angle     :  0.634  10.002  12511  Z= 0.338
  Chirality :  0.045   0.180   1408
  Planarity :  0.004   0.044   1573
  Dihedral  :  5.383  45.453   1275
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 10.68 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: 1131
  helix:  1.78 (0.26), residues: 419
  sheet:  0.85 (0.31), residues: 267
  loop : -0.02 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R  51 
 HIS   0.007   0.002   HIS B 142 
 PHE   0.019   0.002   PHE B 151 
 TYR   0.021   0.002   TYR S 178 
 ARG   0.007   0.001   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.023 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7231 (ptt180) cc_final: 0.6952 (mtt90)
REVERT: R  285 LEU cc_start: 0.8126 (mt) cc_final: 0.7904 (mm)
REVERT: A   24 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7412 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7036 (tt0)
REVERT: A  192 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7149 (mptt)
REVERT: A  209 LYS cc_start: 0.8365 (ptmm) cc_final: 0.7687 (mmmm)
REVERT: A  246 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.7169 (m)
REVERT: B  226 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7852 (mm-30)
REVERT: S   76 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7546 (mptt)
  outliers start: 28
  outliers final: 13
  residues processed: 148
  average time/residue: 1.5713
  time to fit residues: 245.3161
Evaluate side-chains
  146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  192 LYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  198 THR
Chi-restraints excluded: chain S residue  212 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 75 optimal weight:    0.4980
   chunk 16 optimal weight:    0.4980
   chunk 98 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.131327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.105487 restraints weight = 12539.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.90
r_work: 0.3212 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9237  Z= 0.159
  Angle     :  0.535   8.657  12511  Z= 0.287
  Chirality :  0.042   0.159   1408
  Planarity :  0.004   0.044   1573
  Dihedral  :  4.932  39.896   1275
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.00 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.35 (0.26), residues: 1131
  helix:  1.98 (0.26), residues: 420
  sheet:  0.85 (0.31), residues: 269
  loop : -0.06 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.016   0.001   TYR S 178 
 ARG   0.005   0.000   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.012 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7295 (ptt180) cc_final: 0.6949 (mtt90)
REVERT: R  186 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.6983 (m)
REVERT: R  204 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8166 (m)
REVERT: R  285 LEU cc_start: 0.8177 (mt) cc_final: 0.7969 (mm)
REVERT: A   24 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7399 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7018 (tt0)
REVERT: A  186 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7521 (mt-10)
REVERT: A  209 LYS cc_start: 0.8320 (ptmm) cc_final: 0.7607 (mmmm)
REVERT: B   22 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7491 (mpt-90)
REVERT: B   42 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6914 (tpp-160)
  outliers start: 20
  outliers final: 9
  residues processed: 145
  average time/residue: 1.5014
  time to fit residues: 230.1940
Evaluate side-chains
  141 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 LEU
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 72 optimal weight:    8.9990
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.127810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.101942 restraints weight = 12889.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.86
r_work: 0.3168 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9237  Z= 0.265
  Angle     :  0.614   9.476  12511  Z= 0.327
  Chirality :  0.045   0.173   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  5.241  45.050   1275
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.00 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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 (0.26), residues: 1131
  helix:  1.86 (0.26), residues: 420
  sheet:  0.89 (0.31), residues: 266
  loop : -0.14 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R  51 
 HIS   0.005   0.001   HIS B 142 
 PHE   0.017   0.002   PHE B 151 
 TYR   0.022   0.002   TYR S 178 
 ARG   0.009   0.001   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.074 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7277 (ptt180) cc_final: 0.6938 (mtt90)
REVERT: R  186 SER cc_start: 0.7522 (OUTLIER) cc_final: 0.7160 (m)
REVERT: R  204 SER cc_start: 0.8600 (OUTLIER) cc_final: 0.8188 (m)
REVERT: R  285 LEU cc_start: 0.8147 (mt) cc_final: 0.7918 (mm)
REVERT: R  323 MET cc_start: 0.5034 (ttm) cc_final: 0.4549 (ttp)
REVERT: A   24 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7423 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6962 (tt0)
REVERT: A  186 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7490 (mt-10)
REVERT: A  209 LYS cc_start: 0.8339 (ptmm) cc_final: 0.7606 (mmmm)
REVERT: B  226 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7777 (mm-30)
REVERT: S  127 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8286 (t)
  outliers start: 23
  outliers final: 9
  residues processed: 140
  average time/residue: 1.5175
  time to fit residues: 224.2943
Evaluate side-chains
  142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0030
   chunk 7 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 11 optimal weight:    0.2980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.6390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.130482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.105082 restraints weight = 13105.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.99
r_work: 0.3207 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.4086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9237  Z= 0.148
  Angle     :  0.532   8.341  12511  Z= 0.284
  Chirality :  0.042   0.168   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  4.815  38.365   1275
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.02 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.39 (0.26), residues: 1131
  helix:  2.09 (0.26), residues: 420
  sheet:  0.85 (0.31), residues: 269
  loop : -0.12 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 211 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.017   0.001   TYR S 178 
 ARG   0.008   0.000   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 1.026 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7316 (ptt180) cc_final: 0.6912 (mtt90)
REVERT: R  186 SER cc_start: 0.7320 (OUTLIER) cc_final: 0.6929 (m)
REVERT: R  204 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8206 (m)
REVERT: R  285 LEU cc_start: 0.8151 (mt) cc_final: 0.7922 (mm)
REVERT: A   24 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.7336 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6970 (tt0)
REVERT: A  209 LYS cc_start: 0.8275 (ptmm) cc_final: 0.7500 (mmmm)
REVERT: B   42 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6892 (tpp-160)
REVERT: S   76 LYS cc_start: 0.8163 (mmmm) cc_final: 0.7561 (mptt)
REVERT: S  207 LEU cc_start: 0.7895 (tt) cc_final: 0.6989 (pp)
  outliers start: 18
  outliers final: 9
  residues processed: 139
  average time/residue: 1.4627
  time to fit residues: 215.1849
Evaluate side-chains
  141 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 95 optimal weight:   10.0000
   chunk 3 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.129268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.103542 restraints weight = 12850.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 1.87
r_work: 0.3189 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.4094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9237  Z= 0.203
  Angle     :  0.583   8.817  12511  Z= 0.311
  Chirality :  0.043   0.173   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  4.992  43.079   1275
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 13.73 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.31 (0.26), residues: 1131
  helix:  2.01 (0.26), residues: 420
  sheet:  0.82 (0.31), residues: 269
  loop : -0.16 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.014   0.002   PHE B 151 
 TYR   0.021   0.001   TYR S 178 
 ARG   0.009   0.000   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.971 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7362 (ptt180) cc_final: 0.6921 (mtt90)
REVERT: R  186 SER cc_start: 0.7486 (OUTLIER) cc_final: 0.7090 (m)
REVERT: R  204 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8208 (m)
REVERT: R  285 LEU cc_start: 0.8153 (mt) cc_final: 0.7920 (mm)
REVERT: R  323 MET cc_start: 0.4808 (ttm) cc_final: 0.4253 (ttp)
REVERT: A   24 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.7354 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6957 (tt0)
REVERT: A  209 LYS cc_start: 0.8270 (ptmm) cc_final: 0.7524 (mmmm)
REVERT: B   42 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6927 (tpp-160)
REVERT: B  138 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7769 (mt-10)
REVERT: S   76 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7543 (mptt)
REVERT: S  207 LEU cc_start: 0.7918 (tt) cc_final: 0.7034 (pp)
  outliers start: 18
  outliers final: 10
  residues processed: 139
  average time/residue: 1.5505
  time to fit residues: 228.5277
Evaluate side-chains
  143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  102 CYS
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  177 ILE
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0050
   chunk 6 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    0.5994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.131301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.105799 restraints weight = 12884.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.85
r_work: 0.3235 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9237  Z= 0.147
  Angle     :  0.536   7.849  12511  Z= 0.286
  Chirality :  0.042   0.166   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  4.714  37.880   1275
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.14 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.34 (0.26), residues: 1131
  helix:  2.15 (0.26), residues: 420
  sheet:  0.68 (0.30), residues: 282
  loop : -0.18 (0.32), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE B 151 
 TYR   0.017   0.001   TYR S 178 
 ARG   0.009   0.000   ARG B 134 

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

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

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2262 Ramachandran restraints generated.
    1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.947 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7316 (ptt180) cc_final: 0.6886 (mpt180)
REVERT: R  186 SER cc_start: 0.7318 (OUTLIER) cc_final: 0.6896 (m)
REVERT: R  204 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8151 (m)
REVERT: R  323 MET cc_start: 0.4695 (ttm) cc_final: 0.4304 (ttp)
REVERT: A   24 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.7338 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6958 (tt0)
REVERT: A  209 LYS cc_start: 0.8269 (ptmm) cc_final: 0.7496 (mmmm)
REVERT: B   42 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6923 (tpp-160)
REVERT: S   76 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7534 (mptt)
REVERT: S  182 ASN cc_start: 0.7785 (m110) cc_final: 0.7515 (p0)
REVERT: S  207 LEU cc_start: 0.7931 (tt) cc_final: 0.7013 (pp)
  outliers start: 15
  outliers final: 9
  residues processed: 140
  average time/residue: 1.4133
  time to fit residues: 209.8601
Evaluate side-chains
  143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  102 CYS
Chi-restraints excluded: chain R residue  186 SER
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  240 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  189 PHE
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   42 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  241 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 44 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   chunk 32 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.3588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.127213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.102208 restraints weight = 13026.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.91
r_work: 0.3145 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   9237  Z= 0.309
  Angle     :  0.654   9.355  12511  Z= 0.347
  Chirality :  0.047   0.404   1408
  Planarity :  0.004   0.046   1573
  Dihedral  :  5.269  45.417   1275
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.55 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.15 (0.25), residues: 1131
  helix:  1.84 (0.26), residues: 420
  sheet:  0.82 (0.31), residues: 262
  loop : -0.24 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP R  51 
 HIS   0.007   0.002   HIS S  35 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.026   0.002   TYR S 178 
 ARG   0.011   0.001   ARG B 134 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 8487.31 seconds
wall clock time: 150 minutes 3.37 seconds (9003.37 seconds total)