Starting phenix.real_space_refine
on Thu Mar 13 12:07:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xzi_38797/03_2025/8xzi_38797_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xzi_38797/03_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_38797/03_2025/8xzi_38797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xzi_38797/03_2025/8xzi_38797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xzi_38797/03_2025/8xzi_38797_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xzi_38797/03_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-5624/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: 5.67, per 1000 atoms: 0.63
  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: 2.21
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.17
  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: 3.08

  Time building geometry restraints manager: 2.62 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:             0.590
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     24.570
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:14.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.690
-------------------------------------------------------------------------------
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  : 0.977 
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: 1.4068
  time to fit residues: 312.0637
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  : 0.975 
-------------------------------------------------------------------------------
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: 0.3216 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
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  : 1.093 
Fit side-chains
REVERT: R   30 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8224 (mt)
REVERT: R   62 ARG cc_start: 0.7369 (ptt180) cc_final: 0.6824 (mtt90)
REVERT: R  170 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6937 (p)
REVERT: R  204 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8228 (m)
REVERT: R  271 TYR cc_start: 0.8706 (t80) cc_final: 0.8387 (t80)
REVERT: R  285 LEU cc_start: 0.8106 (mt) cc_final: 0.7901 (mm)
REVERT: A   24 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7429 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7318 (tt0)
REVERT: A  186 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: B  325 MET cc_start: 0.8507 (mmm) cc_final: 0.7934 (tpp)
REVERT: S  132 THR cc_start: 0.7215 (m) cc_final: 0.6994 (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: 1.3633
  time to fit residues: 244.2386
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  : 1.121 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 7 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.3582

-------------------------------------------------------------------------------
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 = 0.130484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.103682 restraints weight = 12747.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 2.04
r_work: 0.3183 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9237  Z= 0.223
  Angle     :  0.605   8.013  12511  Z= 0.326
  Chirality :  0.043   0.170   1408
  Planarity :  0.004   0.042   1573
  Dihedral  :  5.299  42.589   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:  1.42 (0.25), residues: 1131
  helix:  1.81 (0.25), residues: 421
  sheet:  1.02 (0.31), residues: 261
  loop :  0.16 (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   0.017   0.002   PHE B 151 
 TYR   0.014   0.002   TYR R  88 
 ARG   0.009   0.000   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
  167 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 2.770 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7270 (ptt180) cc_final: 0.6785 (mpt180)
REVERT: R  204 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8214 (m)
REVERT: R  285 LEU cc_start: 0.8137 (mt) cc_final: 0.7902 (mm)
REVERT: A   24 ARG cc_start: 0.7822 (ttp-110) cc_final: 0.7416 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7041 (tt0)
REVERT: A  186 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7516 (mt-10)
REVERT: A  192 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7227 (mptt)
REVERT: A  209 LYS cc_start: 0.8272 (ptmm) cc_final: 0.7722 (mmmt)
REVERT: G   58 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7284 (tp30)
REVERT: S  207 LEU cc_start: 0.7966 (tp) cc_final: 0.7754 (tt)
  outliers start: 21
  outliers final: 7
  residues processed: 155
  average time/residue: 1.6319
  time to fit residues: 267.1475
Evaluate side-chains
  143 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 133
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 110 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 109 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0870
   chunk 38 optimal weight:    3.9990
   overall best weight:    3.0166

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.127165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.100352 restraints weight = 12674.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.95
r_work: 0.3135 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   9237  Z= 0.380
  Angle     :  0.704  10.712  12511  Z= 0.375
  Chirality :  0.048   0.192   1408
  Planarity :  0.005   0.042   1573
  Dihedral  :  5.684  46.548   1275
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  :  9.97 %
    Favored  : 86.98 %
  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:  1.08 (0.25), residues: 1131
  helix:  1.48 (0.25), residues: 423
  sheet:  0.84 (0.30), residues: 277
  loop : -0.03 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R  51 
 HIS   0.007   0.002   HIS B 142 
 PHE   0.023   0.003   PHE B 151 
 TYR   0.022   0.002   TYR S 178 
 ARG   0.011   0.001   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
  167 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.927 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7304 (ptt180) cc_final: 0.6947 (mtt90)
REVERT: A   24 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.7443 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7057 (tt0)
REVERT: A  192 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7145 (mptt)
REVERT: A  246 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.7196 (m)
REVERT: S   23 SER cc_start: 0.8245 (t) cc_final: 0.7889 (m)
REVERT: S   76 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7491 (mptt)
  outliers start: 30
  outliers final: 14
  residues processed: 153
  average time/residue: 1.5117
  time to fit residues: 244.1787
Evaluate side-chains
  148 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  204 SER
Chi-restraints excluded: chain R residue  242 LYS
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  241 PHE
Chi-restraints excluded: chain B residue  259 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.129705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.103278 restraints weight = 12770.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.94
r_work: 0.3181 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9237  Z= 0.200
  Angle     :  0.572   9.224  12511  Z= 0.306
  Chirality :  0.043   0.165   1408
  Planarity :  0.004   0.043   1573
  Dihedral  :  5.186  42.169   1275
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.50 %
    Favored  : 86.27 %
  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:  1.26 (0.26), residues: 1131
  helix:  1.84 (0.26), residues: 419
  sheet:  0.84 (0.32), residues: 260
  loop : -0.06 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 211 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.020   0.001   TYR R  90 
 ARG   0.011   0.000   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
  157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 1.015 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7334 (ptt180) cc_final: 0.6928 (mtt90)
REVERT: R  204 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8179 (m)
REVERT: R  285 LEU cc_start: 0.8127 (mt) cc_final: 0.7907 (mm)
REVERT: A   24 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7403 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7066 (tt0)
REVERT: A  209 LYS cc_start: 0.8356 (ptmm) cc_final: 0.7672 (mmmm)
REVERT: A  247 MET cc_start: 0.7959 (mtp) cc_final: 0.7720 (mtm)
REVERT: B   42 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6899 (tpp-160)
REVERT: S   76 LYS cc_start: 0.8148 (mmmm) cc_final: 0.7537 (mptt)
  outliers start: 22
  outliers final: 10
  residues processed: 147
  average time/residue: 1.4926
  time to fit residues: 231.9108
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  : 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  252 SER
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   19 LYS
Chi-restraints excluded: chain S residue   63 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  198 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    0.0570
   chunk 55 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 63 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0020
   chunk 75 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 67 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.0112

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.129789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.103863 restraints weight = 12567.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.90
r_work: 0.3195 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9237  Z= 0.182
  Angle     :  0.560   8.816  12511  Z= 0.300
  Chirality :  0.042   0.153   1408
  Planarity :  0.004   0.044   1573
  Dihedral  :  5.032  41.276   1275
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 12.72 %
    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:  1.32 (0.26), residues: 1131
  helix:  1.97 (0.26), residues: 419
  sheet:  0.80 (0.31), residues: 269
  loop : -0.07 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.021   0.001   TYR R  90 
 ARG   0.012   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
  157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.989 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7325 (ptt180) cc_final: 0.6929 (mtt90)
REVERT: R  186 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7100 (m)
REVERT: R  204 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8174 (m)
REVERT: R  285 LEU cc_start: 0.8150 (mt) cc_final: 0.7897 (mm)
REVERT: R  323 MET cc_start: 0.4797 (mtt) cc_final: 0.4426 (ttp)
REVERT: A   24 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7419 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6991 (tt0)
REVERT: A  186 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7488 (mt-10)
REVERT: A  209 LYS cc_start: 0.8335 (ptmm) cc_final: 0.7601 (mmmm)
REVERT: B   42 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6918 (tpp-160)
  outliers start: 21
  outliers final: 11
  residues processed: 147
  average time/residue: 1.4521
  time to fit residues: 225.5809
Evaluate side-chains
  144 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
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  246 SER
Chi-restraints excluded: chain A residue  252 SER
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   19 LYS
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:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.127112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.101599 restraints weight = 12957.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.93
r_work: 0.3155 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9237  Z= 0.293
  Angle     :  0.636   9.685  12511  Z= 0.337
  Chirality :  0.045   0.184   1408
  Planarity :  0.004   0.044   1573
  Dihedral  :  5.358  45.787   1275
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 12.21 %
    Favored  : 85.05 %
  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:  1.17 (0.26), residues: 1131
  helix:  1.80 (0.26), residues: 420
  sheet:  0.79 (0.31), residues: 267
  loop : -0.15 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R  51 
 HIS   0.006   0.002   HIS S  35 
 PHE   0.018   0.002   PHE B 151 
 TYR   0.023   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
  156 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.976 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7279 (ptt180) cc_final: 0.6890 (mpt180)
REVERT: R  186 SER cc_start: 0.7547 (OUTLIER) cc_final: 0.7214 (m)
REVERT: A   24 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7406 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6989 (tt0)
REVERT: A  186 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7492 (mt-10)
REVERT: A  192 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7915 (mttm)
REVERT: A  209 LYS cc_start: 0.8331 (ptmm) cc_final: 0.7599 (mmmm)
REVERT: A  333 GLN cc_start: 0.8616 (tp40) cc_final: 0.8328 (tp-100)
REVERT: B  226 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7788 (mm-30)
REVERT: S  127 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8341 (t)
REVERT: S  207 LEU cc_start: 0.7936 (tt) cc_final: 0.7076 (pp)
  outliers start: 27
  outliers final: 13
  residues processed: 142
  average time/residue: 1.4986
  time to fit residues: 224.6555
Evaluate side-chains
  146 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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  192 LYS
Chi-restraints excluded: chain A residue  246 SER
Chi-restraints excluded: chain A residue  252 SER
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  277 SER
Chi-restraints excluded: chain S residue   19 LYS
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:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3742 r_free = 0.3742 target = 0.128344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.103045 restraints weight = 13121.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.92
r_work: 0.3180 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9237  Z= 0.208
  Angle     :  0.579   8.733  12511  Z= 0.309
  Chirality :  0.043   0.160   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  5.132  43.348   1275
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.43 %
    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:  1.21 (0.26), residues: 1131
  helix:  1.91 (0.26), residues: 420
  sheet:  0.70 (0.31), residues: 276
  loop : -0.15 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  51 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.015   0.002   PHE B 151 
 TYR   0.022   0.002   TYR R  90 
 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
  150 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.001 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7397 (ptt180) cc_final: 0.6922 (mtt90)
REVERT: R  186 SER cc_start: 0.7542 (OUTLIER) cc_final: 0.7186 (m)
REVERT: R  204 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8194 (m)
REVERT: R  323 MET cc_start: 0.4676 (mtt) cc_final: 0.4356 (ttp)
REVERT: A   24 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7385 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7037 (tt0)
REVERT: A  186 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7496 (mt-10)
REVERT: A  209 LYS cc_start: 0.8298 (ptmm) cc_final: 0.7557 (mmmm)
REVERT: B   42 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6930 (tpp-160)
REVERT: S   76 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7506 (mptt)
REVERT: S  127 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8343 (t)
REVERT: S  207 LEU cc_start: 0.7944 (tt) cc_final: 0.7075 (pp)
  outliers start: 22
  outliers final: 10
  residues processed: 139
  average time/residue: 1.5394
  time to fit residues: 226.4831
Evaluate side-chains
  142 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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  252 SER
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  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue  127 VAL
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:    7.9990
   chunk 3 optimal weight:    0.0980
   chunk 2 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 90 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.129295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.103304 restraints weight = 12897.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.91
r_work: 0.3191 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9237  Z= 0.179
  Angle     :  0.554   7.499  12511  Z= 0.296
  Chirality :  0.042   0.149   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  4.962  41.413   1275
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.69
  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:  1.22 (0.26), residues: 1131
  helix:  2.01 (0.26), residues: 420
  sheet:  0.63 (0.30), residues: 279
  loop : -0.20 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.014   0.001   PHE B 151 
 TYR   0.022   0.001   TYR R  90 
 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
  159 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.977 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7364 (ptt180) cc_final: 0.6948 (mtt90)
REVERT: R  186 SER cc_start: 0.7424 (OUTLIER) cc_final: 0.7035 (m)
REVERT: R  204 SER cc_start: 0.8607 (OUTLIER) cc_final: 0.8184 (m)
REVERT: R  323 MET cc_start: 0.4621 (mtt) cc_final: 0.4357 (ttp)
REVERT: A   24 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7399 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7015 (tt0)
REVERT: A  186 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7489 (mt-10)
REVERT: A  209 LYS cc_start: 0.8292 (ptmm) cc_final: 0.7555 (mmmm)
REVERT: B   42 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6965 (tpp-160)
REVERT: B  138 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7758 (mt-10)
REVERT: S   76 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7587 (mptt)
REVERT: S  207 LEU cc_start: 0.7966 (tt) cc_final: 0.7092 (pp)
  outliers start: 18
  outliers final: 10
  residues processed: 149
  average time/residue: 1.4445
  time to fit residues: 227.4525
Evaluate side-chains
  147 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
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  252 SER
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  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain S residue   19 LYS
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:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3757 r_free = 0.3757 target = 0.129409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.104228 restraints weight = 12942.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.86
r_work: 0.3201 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9237  Z= 0.174
  Angle     :  0.564   7.276  12511  Z= 0.299
  Chirality :  0.043   0.313   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  4.929  41.371   1275
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.85 %
    Favored  : 83.52 %
  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:  1.26 (0.26), residues: 1131
  helix:  2.05 (0.26), residues: 420
  sheet:  0.68 (0.30), residues: 279
  loop : -0.22 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.001   PHE B 151 
 TYR   0.021   0.001   TYR R  90 
 ARG   0.010   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
  154 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 1.073 
Fit side-chains
REVERT: R   62 ARG cc_start: 0.7393 (ptt180) cc_final: 0.6949 (mtt90)
REVERT: R  186 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.6992 (m)
REVERT: R  204 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8174 (m)
REVERT: R  271 TYR cc_start: 0.8671 (t80) cc_final: 0.8395 (t80)
REVERT: R  323 MET cc_start: 0.4542 (mtt) cc_final: 0.4285 (ttp)
REVERT: A   24 ARG cc_start: 0.7764 (ttp-110) cc_final: 0.7366 (ttp-110)
REVERT: A   33 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6963 (tt0)
REVERT: A  209 LYS cc_start: 0.8296 (ptmm) cc_final: 0.7537 (mmmm)
REVERT: B   42 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6958 (tpp-160)
REVERT: B  138 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7753 (mt-10)
REVERT: S   76 LYS cc_start: 0.8110 (mmmm) cc_final: 0.7568 (mptt)
REVERT: S  207 LEU cc_start: 0.7955 (tt) cc_final: 0.7067 (pp)
  outliers start: 16
  outliers final: 10
  residues processed: 144
  average time/residue: 1.4565
  time to fit residues: 221.9908
Evaluate side-chains
  149 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
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  252 SER
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  270 ILE
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:    0.0770
   chunk 39 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 101 optimal weight:    0.3980
   chunk 6 optimal weight:    2.9990
   chunk 86 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.0940

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.129157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.103778 restraints weight = 13016.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 2.00
r_work: 0.3187 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9237  Z= 0.189
  Angle     :  0.571   7.011  12511  Z= 0.304
  Chirality :  0.043   0.186   1408
  Planarity :  0.004   0.045   1573
  Dihedral  :  4.959  42.324   1275
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.06 %
    Favored  : 83.21 %
  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:  1.26 (0.25), residues: 1131
  helix:  2.05 (0.26), residues: 420
  sheet:  0.85 (0.31), residues: 262
  loop : -0.30 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.013   0.002   PHE B 151 
 TYR   0.022   0.001   TYR R  90 
 ARG   0.010   0.000   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: 8894.09 seconds
wall clock time: 154 minutes 6.05 seconds (9246.05 seconds total)