Starting phenix.real_space_refine
on Thu Feb 13 10:18:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ezm_31389/02_2025/7ezm_31389.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ezm_31389/02_2025/7ezm_31389.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ezm_31389/02_2025/7ezm_31389.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ezm_31389/02_2025/7ezm_31389.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ezm_31389/02_2025/7ezm_31389.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ezm_31389/02_2025/7ezm_31389.cif"
  }
  resolution = 2.9
  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=   0.032
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      69      5.16       5
     C    5748      2.51       5
     N    1524      2.21       5
     O    1667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9008
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1850
          Classifications: {'peptide': 227}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "B"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2561
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 2362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2362
          Classifications: {'peptide': 304}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 12, 'TRANS': 291}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 44
    Chain: "G"
      Number of atoms: 421
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 421
          Classifications: {'peptide': 59}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 54}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "H"
      Number of atoms: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1736
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 60
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "P"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 8
  Time building chain proxies: 5.45, per 1000 atoms: 0.61
  Number of scatterers: 9008
  At special positions: 0
  Unit cell: (104.5, 120.175, 121.22, 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      69     16.00
     O    1667      8.00
     N    1524      7.00
     C    5748      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 114 " - pdb=" SG  CYS D 196 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.05

  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: 2.52
  Conformation dependent library (CDL) restraints added in 919.0 milliseconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 13 sheets defined
      40.1% alpha, 21.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 38
    Processing helix  chain 'A' and resid 51 through 63
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.595A  pdb=" N   ILE A 217 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   HIS A 218 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 236
    Processing helix  chain 'A' and resid 246 through 261
    Processing helix  chain 'A' and resid 262 through 266
      removed outlier: 3.550A  pdb=" N   GLN A 265 " --> pdb=" O   PRO A 262 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ASN A 266 " --> pdb=" O   TRP A 263 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 262 through 266'
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'A' and resid 287 through 291
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'B' and resid 6 through 26
      removed outlier: 4.209A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'D' and resid 39 through 69
    Processing helix  chain 'D' and resid 70 through 73
    Processing helix  chain 'D' and resid 74 through 105
      Proline residue:  D  96  - end of helix
      Proline residue:  D 101  - end of helix
    Processing helix  chain 'D' and resid 110 through 145
    Processing helix  chain 'D' and resid 147 through 152
    Processing helix  chain 'D' and resid 154 through 173
    Processing helix  chain 'D' and resid 174 through 180
      removed outlier: 3.595A  pdb=" N   ILE D 178 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 217
    Processing helix  chain 'D' and resid 218 through 248
    Processing helix  chain 'D' and resid 301 through 339
      Proline residue:  D 328  - end of helix
    Processing helix  chain 'D' and resid 339 through 348
    Processing helix  chain 'D' and resid 349 through 371
      removed outlier: 4.019A  pdb=" N   SER D 363 " --> pdb=" O   SER D 359 " (cutoff:3.500A)
      Proline residue:  D 367  - end of helix
    Processing helix  chain 'D' and resid 374 through 383
    Processing helix  chain 'G' and resid 9 through 25
      removed outlier: 3.849A  pdb=" N   LEU G  15 " --> pdb=" O   GLN G  11 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE G  25 " --> pdb=" O   MET G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 52 through 56
      removed outlier: 4.106A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196
      removed outlier: 6.662A  pdb=" N   LEU A  40 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   VAL A 204 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU A  42 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER A 225 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ILE A 226 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   PHE A 272 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   PHE A 228 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ASN A 274 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   VAL A 230 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.882A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.675A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.354A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.814A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.649A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.827A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 186
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.063A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148
      removed outlier: 3.507A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)

    482 hydrogen bonds defined for protein.
    1335 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: 2.80

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2088
        1.33 -     1.46: 2829
        1.46 -     1.60: 4172
        1.60 -     1.73: 1
        1.73 -     1.86: 106
  Bond restraints: 9196
  Sorted by residual:
  bond pdb=" O1  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.462  1.636 -0.174 2.00e-02 2.50e+03 7.56e+01
  bond pdb=" OH  TYS P   2 "
       pdb=" S   TYS P   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.526  0.153 2.00e-02 2.50e+03 5.81e+01
  bond pdb=" CA  SER B 281 "
       pdb=" CB  SER B 281 "
    ideal  model  delta    sigma   weight residual
    1.532  1.465  0.066 1.78e-02 3.16e+03 1.39e+01
  bond pdb=" N   VAL A 240 "
       pdb=" CA  VAL A 240 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.033 1.19e-02 7.06e+03 7.60e+00
  bond pdb=" N   GLY B  41 "
       pdb=" CA  GLY B  41 "
    ideal  model  delta    sigma   weight residual
    1.448  1.492 -0.044 1.88e-02 2.83e+03 5.56e+00
  ... (remaining 9191 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 11457
        1.81 -     3.62: 914
        3.62 -     5.43: 91
        5.43 -     7.24: 18
        7.24 -     9.05: 4
  Bond angle restraints: 12484
  Sorted by residual:
  angle pdb=" C   ARG D 139 "
        pdb=" CA  ARG D 139 "
        pdb=" CB  ARG D 139 "
      ideal   model   delta    sigma   weight residual
     110.68  118.72   -8.04 1.70e+00 3.46e-01 2.23e+01
  angle pdb=" C   ARG D 345 "
        pdb=" CA  ARG D 345 "
        pdb=" CB  ARG D 345 "
      ideal   model   delta    sigma   weight residual
     110.88  103.83    7.05 1.57e+00 4.06e-01 2.02e+01
  angle pdb=" N   VAL A 238 "
        pdb=" CA  VAL A 238 "
        pdb=" C   VAL A 238 "
      ideal   model   delta    sigma   weight residual
     109.20  102.41    6.79 1.55e+00 4.16e-01 1.92e+01
  angle pdb=" N   ALA H 136 "
        pdb=" CA  ALA H 136 "
        pdb=" C   ALA H 136 "
      ideal   model   delta    sigma   weight residual
     113.02  107.99    5.03 1.20e+00 6.94e-01 1.75e+01
  angle pdb=" CA  VAL A 238 "
        pdb=" C   VAL A 238 "
        pdb=" O   VAL A 238 "
      ideal   model   delta    sigma   weight residual
     121.92  117.04    4.88 1.17e+00 7.31e-01 1.74e+01
  ... (remaining 12479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.36: 4939
       16.36 -    32.71: 413
       32.71 -    49.06: 76
       49.06 -    65.42: 22
       65.42 -    81.77: 5
  Dihedral angle restraints: 5455
    sinusoidal: 2051
      harmonic: 3404
  Sorted by residual:
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.95  -63.95     1      1.00e+01 1.00e-02 5.38e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.59   28.41     0      5.00e+00 4.00e-02 3.23e+01
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.84   27.16     0      5.00e+00 4.00e-02 2.95e+01
  ... (remaining 5452 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1137
       0.081 -    0.163: 272
       0.163 -    0.244: 23
       0.244 -    0.325: 3
       0.325 -    0.407: 2
  Chirality restraints: 1437
  Sorted by residual:
  chirality pdb=" CA  ARG A 210 "
            pdb=" N   ARG A 210 "
            pdb=" C   ARG A 210 "
            pdb=" CB  ARG A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.92   -0.41 2.00e-01 2.50e+01 4.14e+00
  chirality pdb=" CA  ARG D 345 "
            pdb=" N   ARG D 345 "
            pdb=" C   ARG D 345 "
            pdb=" CB  ARG D 345 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" CG  LEU A 316 "
            pdb=" CB  LEU A 316 "
            pdb=" CD1 LEU A 316 "
            pdb=" CD2 LEU A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1434 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 313 "    0.048 9.50e-02 1.11e+02   4.23e-02 1.69e+01
        pdb=" NE  ARG D 313 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 313 "    0.070 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 313 "   -0.024 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 313 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO D 367 "   -0.020 2.00e-02 2.50e+03   4.08e-02 1.67e+01
        pdb=" C   PRO D 367 "    0.071 2.00e-02 2.50e+03
        pdb=" O   PRO D 367 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ILE D 368 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 202 "   -0.006 9.50e-02 1.11e+02   3.17e-02 1.25e+01
        pdb=" NE  ARG A 202 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 202 "   -0.061 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 202 "    0.021 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 202 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1292
        2.76 -     3.30: 9206
        3.30 -     3.83: 15416
        3.83 -     4.37: 19126
        4.37 -     4.90: 32178
  Nonbonded interactions: 77218
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 356 "
            pdb=" OE1 GLN D 153 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   TYR D 360 "
            pdb=" OG  SER D 363 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   MET D  72 "
            pdb=" ND2 ASN D  77 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN D  98 "
            pdb=" OH  TYR D 360 "
     model   vdw
     2.260 3.040
  ... (remaining 77213 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:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     23.230
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:12.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
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      :  0.011   0.174   9196  Z= 0.684
  Angle     :  1.074   9.054  12484  Z= 0.645
  Chirality :  0.068   0.407   1437
  Planarity :  0.009   0.102   1576
  Dihedral  : 13.160  81.772   3241
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  3.34 %
    Favored  : 95.72 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -0.87 (0.23), residues: 1150
  helix: -0.43 (0.23), residues: 404
  sheet: -0.10 (0.30), residues: 278
  loop : -0.83 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.008   TRP B  82 
 HIS   0.019   0.006   HIS D 157 
 PHE   0.025   0.006   PHE B 241 
 TYR   0.046   0.009   TYR H 175 
 ARG   0.071   0.009   ARG D 313 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 308
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.7426 (p) cc_final: 0.6994 (p)
REVERT: A    9 ASP cc_start: 0.6886 (m-30) cc_final: 0.6420 (m-30)
REVERT: A   39 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6529 (mt-10)
REVERT: A  237 GLN cc_start: 0.7324 (mt0) cc_final: 0.7086 (mt0)
REVERT: A  275 LYS cc_start: 0.7832 (mttt) cc_final: 0.7625 (mttt)
REVERT: B   67 SER cc_start: 0.7986 (m) cc_final: 0.7689 (t)
REVERT: B   74 SER cc_start: 0.7782 (t) cc_final: 0.7454 (t)
REVERT: B   98 SER cc_start: 0.7826 (p) cc_final: 0.7445 (t)
REVERT: B  118 ASP cc_start: 0.6246 (p0) cc_final: 0.5987 (p0)
REVERT: B  184 THR cc_start: 0.8506 (p) cc_final: 0.8296 (t)
REVERT: B  220 GLN cc_start: 0.8247 (mt0) cc_final: 0.7890 (mt0)
REVERT: B  221 THR cc_start: 0.7915 (m) cc_final: 0.7714 (t)
REVERT: B  277 SER cc_start: 0.8359 (t) cc_final: 0.8149 (t)
REVERT: B  334 SER cc_start: 0.7768 (m) cc_final: 0.7554 (p)
REVERT: D   76 THR cc_start: 0.7375 (m) cc_final: 0.7143 (m)
REVERT: D  111 SER cc_start: 0.8252 (t) cc_final: 0.8007 (p)
REVERT: H  141 THR cc_start: 0.7753 (m) cc_final: 0.7420 (p)
REVERT: H  180 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7688 (mtt180)
  outliers start: 9
  outliers final: 4
  residues processed: 315
  average time/residue: 1.1212
  time to fit residues: 378.1937
Evaluate side-chains
  277 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 273
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  244 ASN
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  250 GLU
Chi-restraints excluded: chain H residue  135 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 85 optimal weight:    7.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0170
   chunk 88 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
B 132 ASN
D 131 ASN
D 374 ASN
H 142 GLN
H 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.136454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.122441 restraints weight = 12166.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.91
r_work: 0.3370 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9196  Z= 0.232
  Angle     :  0.620   6.811  12484  Z= 0.329
  Chirality :  0.045   0.164   1437
  Planarity :  0.004   0.042   1576
  Dihedral  :  6.901  72.494   1271
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 13.36 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.55 (0.25), residues: 1150
  helix:  1.35 (0.26), residues: 409
  sheet: -0.23 (0.29), residues: 282
  loop :  0.02 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.033   0.002   PHE A  55 
 TYR   0.014   0.002   TYR H 190 
 ARG   0.008   0.001   ARG D 345 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 272
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8202 (p) cc_final: 0.7885 (p)
REVERT: A   39 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7399 (mt-10)
REVERT: A  201 PHE cc_start: 0.8320 (m-80) cc_final: 0.7826 (m-80)
REVERT: A  212 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7674 (mt-10)
REVERT: A  276 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7389 (ptpp)
REVERT: A  290 ASP cc_start: 0.7586 (m-30) cc_final: 0.7372 (m-30)
REVERT: B   52 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7519 (ptp90)
REVERT: B   68 ARG cc_start: 0.8147 (ttt180) cc_final: 0.7786 (ttt180)
REVERT: B   98 SER cc_start: 0.7718 (p) cc_final: 0.7334 (t)
REVERT: B  161 SER cc_start: 0.7550 (m) cc_final: 0.7345 (p)
REVERT: B  170 ASP cc_start: 0.7733 (t70) cc_final: 0.7349 (OUTLIER)
REVERT: B  186 ASP cc_start: 0.6992 (t0) cc_final: 0.6746 (t0)
REVERT: B  214 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7492 (mtm-85)
REVERT: B  268 ASN cc_start: 0.7631 (p0) cc_final: 0.7405 (p0)
REVERT: B  271 CYS cc_start: 0.7854 (m) cc_final: 0.7557 (p)
REVERT: D   77 ASN cc_start: 0.8173 (m-40) cc_final: 0.7948 (m-40)
REVERT: D   85 VAL cc_start: 0.8387 (t) cc_final: 0.8135 (p)
REVERT: D  126 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8387 (m)
REVERT: D  202 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7507 (p0)
REVERT: D  308 LYS cc_start: 0.8220 (mmtp) cc_final: 0.7964 (mttm)
REVERT: D  344 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7606 (mt-10)
REVERT: H   34 MET cc_start: 0.8542 (mmt) cc_final: 0.8308 (mmm)
REVERT: H   68 PHE cc_start: 0.7239 (m-10) cc_final: 0.6680 (m-80)
REVERT: H   78 THR cc_start: 0.8416 (t) cc_final: 0.7820 (m)
REVERT: H  141 THR cc_start: 0.7988 (m) cc_final: 0.7616 (p)
REVERT: H  180 ARG cc_start: 0.8351 (mtt180) cc_final: 0.7979 (mtt180)
REVERT: P    8 PHE cc_start: 0.8395 (m-10) cc_final: 0.8149 (m-10)
  outliers start: 45
  outliers final: 23
  residues processed: 290
  average time/residue: 1.1353
  time to fit residues: 352.6589
Evaluate side-chains
  264 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 239
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  314 VAL
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue  126 SER
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  202 ASN
Chi-restraints excluded: chain D residue  304 ASN
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue  135 SER
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 102 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
D 374 ASN
G  18 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.133416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.118963 restraints weight = 12275.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.95
r_work: 0.3318 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9196  Z= 0.289
  Angle     :  0.603   6.969  12484  Z= 0.317
  Chirality :  0.045   0.153   1437
  Planarity :  0.004   0.043   1576
  Dihedral  :  5.599  69.130   1263
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 16.39 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.64 (0.25), residues: 1150
  helix:  1.48 (0.25), residues: 417
  sheet: -0.24 (0.29), residues: 276
  loop :  0.02 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 339 
 HIS   0.005   0.001   HIS B  62 
 PHE   0.031   0.002   PHE A  55 
 TYR   0.016   0.002   TYR D 179 
 ARG   0.008   0.001   ARG B 129 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 248
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8408 (p) cc_final: 0.8048 (p)
REVERT: A    9 ASP cc_start: 0.7994 (m-30) cc_final: 0.7618 (m-30)
REVERT: A   17 LYS cc_start: 0.8115 (mttm) cc_final: 0.7913 (mmtp)
REVERT: A   39 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7394 (mt-10)
REVERT: A  201 PHE cc_start: 0.8445 (m-80) cc_final: 0.7874 (m-80)
REVERT: A  276 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7513 (ptpp)
REVERT: A  290 ASP cc_start: 0.7704 (m-30) cc_final: 0.7418 (m-30)
REVERT: A  307 GLU cc_start: 0.8043 (tp30) cc_final: 0.7740 (tp30)
REVERT: B   52 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7477 (mtp85)
REVERT: B   87 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7807 (t)
REVERT: B   98 SER cc_start: 0.8001 (p) cc_final: 0.7664 (t)
REVERT: B  212 ASP cc_start: 0.7692 (t70) cc_final: 0.7454 (t0)
REVERT: B  214 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7495 (mtm180)
REVERT: B  271 CYS cc_start: 0.8037 (m) cc_final: 0.7694 (p)
REVERT: B  274 THR cc_start: 0.8063 (m) cc_final: 0.7752 (p)
REVERT: B  289 TYR cc_start: 0.7661 (m-10) cc_final: 0.7124 (m-80)
REVERT: D  202 ASN cc_start: 0.8069 (p0) cc_final: 0.7822 (p0)
REVERT: D  308 LYS cc_start: 0.8282 (mmtp) cc_final: 0.8028 (mttp)
REVERT: D  336 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7922 (ttt180)
REVERT: D  344 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7682 (mt-10)
REVERT: H   68 PHE cc_start: 0.7371 (m-10) cc_final: 0.6927 (m-10)
REVERT: H  180 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8284 (mtt180)
  outliers start: 45
  outliers final: 23
  residues processed: 269
  average time/residue: 1.1201
  time to fit residues: 322.3810
Evaluate side-chains
  258 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 232
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  268 ASN
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   23 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
H 194 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.115675 restraints weight = 12081.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.93
r_work: 0.3308 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9196  Z= 0.277
  Angle     :  0.579   7.159  12484  Z= 0.304
  Chirality :  0.044   0.145   1437
  Planarity :  0.004   0.044   1576
  Dihedral  :  5.451  70.009   1262
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 17.54 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.69 (0.25), residues: 1150
  helix:  1.68 (0.25), residues: 409
  sheet: -0.28 (0.29), residues: 285
  loop : -0.04 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B  62 
 PHE   0.028   0.002   PHE A  55 
 TYR   0.017   0.002   TYR D 179 
 ARG   0.007   0.000   ARG A  38 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 237
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8463 (p) cc_final: 0.8102 (p)
REVERT: A    9 ASP cc_start: 0.8012 (m-30) cc_final: 0.7636 (m-30)
REVERT: A   17 LYS cc_start: 0.8138 (mttm) cc_final: 0.7928 (mmtp)
REVERT: A   39 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7233 (mt-10)
REVERT: A  201 PHE cc_start: 0.8459 (m-80) cc_final: 0.7849 (m-80)
REVERT: A  202 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.8027 (ttm-80)
REVERT: A  276 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7528 (ptpp)
REVERT: A  290 ASP cc_start: 0.7712 (m-30) cc_final: 0.7384 (m-30)
REVERT: A  307 GLU cc_start: 0.8079 (tp30) cc_final: 0.7723 (tp30)
REVERT: A  322 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7851 (ttmm)
REVERT: B   52 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7224 (mtt90)
REVERT: B   98 SER cc_start: 0.8033 (p) cc_final: 0.7682 (t)
REVERT: B  212 ASP cc_start: 0.7741 (t70) cc_final: 0.7491 (t0)
REVERT: B  268 ASN cc_start: 0.7936 (p0) cc_final: 0.7645 (p0)
REVERT: B  271 CYS cc_start: 0.8070 (m) cc_final: 0.7746 (p)
REVERT: B  274 THR cc_start: 0.7987 (m) cc_final: 0.7708 (p)
REVERT: B  289 TYR cc_start: 0.7747 (m-10) cc_final: 0.7006 (m-80)
REVERT: B  312 ASP cc_start: 0.7614 (t0) cc_final: 0.7354 (t70)
REVERT: D   67 ILE cc_start: 0.7556 (pt) cc_final: 0.7289 (mm)
REVERT: D   74 THR cc_start: 0.8055 (t) cc_final: 0.7647 (p)
REVERT: D   75 VAL cc_start: 0.8148 (p) cc_final: 0.7696 (t)
REVERT: D  202 ASN cc_start: 0.8120 (p0) cc_final: 0.7899 (p0)
REVERT: D  308 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8129 (mttm)
REVERT: D  323 PHE cc_start: 0.8616 (m-80) cc_final: 0.8154 (m-80)
REVERT: D  336 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8022 (ttt180)
REVERT: D  344 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7720 (mt-10)
REVERT: H   20 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7718 (pp)
REVERT: H   30 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8187 (t)
REVERT: H   63 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8210 (t)
  outliers start: 45
  outliers final: 23
  residues processed: 261
  average time/residue: 1.1950
  time to fit residues: 333.3955
Evaluate side-chains
  262 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 234
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  210 ARG
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain D residue   53 LEU
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   23 SER
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0010
   chunk 67 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 112 optimal weight:    0.0970
   chunk 86 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 350 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.129840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115391 restraints weight = 12142.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.94
r_work: 0.3342 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.3457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9196  Z= 0.173
  Angle     :  0.544   9.411  12484  Z= 0.284
  Chirality :  0.042   0.161   1437
  Planarity :  0.004   0.041   1576
  Dihedral  :  5.215  70.890   1262
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.04 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.82 (0.25), residues: 1150
  helix:  1.93 (0.25), residues: 409
  sheet: -0.25 (0.29), residues: 288
  loop : -0.10 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 339 
 HIS   0.003   0.001   HIS D 210 
 PHE   0.025   0.001   PHE A  55 
 TYR   0.016   0.001   TYR D 179 
 ARG   0.006   0.000   ARG A  38 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 246
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8423 (p) cc_final: 0.8158 (p)
REVERT: A    9 ASP cc_start: 0.7946 (m-30) cc_final: 0.7634 (m-30)
REVERT: A   39 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7344 (mt-10)
REVERT: A  201 PHE cc_start: 0.8480 (m-80) cc_final: 0.7656 (m-80)
REVERT: A  276 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7526 (ttpp)
REVERT: A  290 ASP cc_start: 0.7698 (m-30) cc_final: 0.7357 (m-30)
REVERT: A  307 GLU cc_start: 0.8080 (tp30) cc_final: 0.7757 (tp30)
REVERT: A  322 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7795 (ttmm)
REVERT: B   33 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7677 (mt)
REVERT: B   52 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7206 (mtt90)
REVERT: B   61 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7836 (ppp)
REVERT: B   98 SER cc_start: 0.7857 (p) cc_final: 0.7512 (t)
REVERT: B  170 ASP cc_start: 0.7955 (t70) cc_final: 0.7521 (t0)
REVERT: B  212 ASP cc_start: 0.7688 (t70) cc_final: 0.7444 (t0)
REVERT: B  227 SER cc_start: 0.8584 (m) cc_final: 0.8054 (t)
REVERT: B  271 CYS cc_start: 0.8036 (m) cc_final: 0.7752 (p)
REVERT: B  289 TYR cc_start: 0.7588 (m-10) cc_final: 0.7372 (m-80)
REVERT: B  312 ASP cc_start: 0.7593 (t0) cc_final: 0.7341 (t70)
REVERT: D   67 ILE cc_start: 0.7499 (pt) cc_final: 0.7251 (mm)
REVERT: D   74 THR cc_start: 0.8052 (t) cc_final: 0.7717 (p)
REVERT: D   75 VAL cc_start: 0.8215 (p) cc_final: 0.7723 (t)
REVERT: D  170 PHE cc_start: 0.7079 (m-10) cc_final: 0.6799 (m-10)
REVERT: D  202 ASN cc_start: 0.8141 (p0) cc_final: 0.7926 (p0)
REVERT: D  323 PHE cc_start: 0.8587 (m-80) cc_final: 0.8174 (m-80)
REVERT: D  329 ILE cc_start: 0.8458 (tp) cc_final: 0.8224 (tt)
REVERT: D  336 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7942 (ttt180)
REVERT: H   63 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8103 (t)
REVERT: H  214 LEU cc_start: 0.8031 (tp) cc_final: 0.7823 (tt)
  outliers start: 33
  outliers final: 18
  residues processed: 260
  average time/residue: 1.2001
  time to fit residues: 333.3987
Evaluate side-chains
  258 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 235
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  276 LYS
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  234 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  346 ARG
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 96 optimal weight:    0.3980
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.129409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115336 restraints weight = 11966.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.89
r_work: 0.3330 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9196  Z= 0.259
  Angle     :  0.565   9.318  12484  Z= 0.295
  Chirality :  0.043   0.145   1437
  Planarity :  0.004   0.041   1576
  Dihedral  :  5.253  70.138   1262
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 19.42 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.79 (0.25), residues: 1150
  helix:  1.86 (0.25), residues: 412
  sheet: -0.21 (0.29), residues: 286
  loop : -0.12 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.004   0.001   HIS D 210 
 PHE   0.025   0.002   PHE A  55 
 TYR   0.015   0.002   TYR D 179 
 ARG   0.007   0.000   ARG A  38 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 241
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8485 (p) cc_final: 0.8231 (p)
REVERT: A    9 ASP cc_start: 0.7951 (m-30) cc_final: 0.7668 (m-30)
REVERT: A   39 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7172 (mt-10)
REVERT: A  201 PHE cc_start: 0.8498 (m-80) cc_final: 0.7684 (m-80)
REVERT: A  202 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8024 (ttm-80)
REVERT: A  290 ASP cc_start: 0.7722 (m-30) cc_final: 0.7389 (m-30)
REVERT: A  307 GLU cc_start: 0.8051 (tp30) cc_final: 0.7718 (tp30)
REVERT: A  322 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7766 (ttmm)
REVERT: B   52 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7434 (mtp85)
REVERT: B   61 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7841 (tmm)
REVERT: B   87 THR cc_start: 0.8199 (m) cc_final: 0.7910 (t)
REVERT: B   98 SER cc_start: 0.8006 (p) cc_final: 0.7658 (t)
REVERT: B  212 ASP cc_start: 0.7674 (t70) cc_final: 0.7445 (t0)
REVERT: B  227 SER cc_start: 0.8598 (m) cc_final: 0.8096 (t)
REVERT: B  271 CYS cc_start: 0.8063 (m) cc_final: 0.7753 (p)
REVERT: B  289 TYR cc_start: 0.7744 (m-10) cc_final: 0.7301 (m-80)
REVERT: B  312 ASP cc_start: 0.7641 (t0) cc_final: 0.7389 (t70)
REVERT: D   74 THR cc_start: 0.8029 (t) cc_final: 0.7697 (p)
REVERT: D   75 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7751 (t)
REVERT: D  202 ASN cc_start: 0.8156 (p0) cc_final: 0.7931 (p0)
REVERT: D  323 PHE cc_start: 0.8613 (m-80) cc_final: 0.8114 (m-80)
REVERT: D  329 ILE cc_start: 0.8446 (tp) cc_final: 0.8226 (tt)
REVERT: D  336 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8001 (ttt180)
REVERT: H   63 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8233 (t)
REVERT: H  199 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8122 (m)
  outliers start: 42
  outliers final: 23
  residues processed: 261
  average time/residue: 1.1726
  time to fit residues: 327.5730
Evaluate side-chains
  263 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 235
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  346 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0370
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.9264

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
D 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.128221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.114014 restraints weight = 12205.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.92
r_work: 0.3325 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9196  Z= 0.277
  Angle     :  0.583   8.663  12484  Z= 0.301
  Chirality :  0.044   0.197   1437
  Planarity :  0.004   0.041   1576
  Dihedral  :  5.293  69.810   1262
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 19.83 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.76 (0.25), residues: 1150
  helix:  1.84 (0.25), residues: 411
  sheet: -0.19 (0.30), residues: 279
  loop : -0.16 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 339 
 HIS   0.004   0.001   HIS D 210 
 PHE   0.028   0.002   PHE A  55 
 TYR   0.017   0.002   TYR D 179 
 ARG   0.007   0.001   ARG A  38 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 243
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8529 (p) cc_final: 0.8293 (p)
REVERT: A    9 ASP cc_start: 0.7969 (m-30) cc_final: 0.7708 (m-30)
REVERT: A   39 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7316 (mt-10)
REVERT: A  201 PHE cc_start: 0.8530 (m-80) cc_final: 0.7682 (m-80)
REVERT: A  290 ASP cc_start: 0.7746 (m-30) cc_final: 0.7420 (m-30)
REVERT: A  294 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7560 (mm-30)
REVERT: A  307 GLU cc_start: 0.7999 (tp30) cc_final: 0.7688 (tp30)
REVERT: A  322 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7881 (ttmp)
REVERT: A  341 PHE cc_start: 0.8588 (t80) cc_final: 0.8048 (t80)
REVERT: B   98 SER cc_start: 0.8138 (p) cc_final: 0.7815 (t)
REVERT: B  212 ASP cc_start: 0.7699 (t70) cc_final: 0.7439 (t0)
REVERT: B  220 GLN cc_start: 0.8354 (mt0) cc_final: 0.8058 (mt0)
REVERT: B  227 SER cc_start: 0.8559 (m) cc_final: 0.8059 (t)
REVERT: B  271 CYS cc_start: 0.8054 (m) cc_final: 0.7714 (p)
REVERT: B  312 ASP cc_start: 0.7650 (t0) cc_final: 0.7384 (t70)
REVERT: D   67 ILE cc_start: 0.7593 (pt) cc_final: 0.7269 (mm)
REVERT: D   74 THR cc_start: 0.8014 (t) cc_final: 0.7713 (p)
REVERT: D   75 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.7856 (t)
REVERT: D  115 LYS cc_start: 0.8454 (mmmt) cc_final: 0.7662 (mmpt)
REVERT: D  202 ASN cc_start: 0.8207 (p0) cc_final: 0.7993 (p0)
REVERT: D  213 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8056 (mp)
REVERT: D  323 PHE cc_start: 0.8606 (m-80) cc_final: 0.8096 (m-80)
REVERT: D  329 ILE cc_start: 0.8431 (tp) cc_final: 0.8216 (tt)
REVERT: D  336 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7966 (ttt180)
REVERT: H   30 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8166 (t)
REVERT: H   63 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8242 (t)
REVERT: H  145 SER cc_start: 0.7902 (t) cc_final: 0.7684 (t)
  outliers start: 44
  outliers final: 27
  residues processed: 267
  average time/residue: 1.1029
  time to fit residues: 315.9933
Evaluate side-chains
  270 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 238
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   20 LEU
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain H residue  238 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 102 optimal weight:    0.2980
   chunk 71 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 77 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
D 304 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.128864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.114781 restraints weight = 12221.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.90
r_work: 0.3341 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   9196  Z= 0.220
  Angle     :  0.567   8.411  12484  Z= 0.292
  Chirality :  0.043   0.193   1437
  Planarity :  0.004   0.041   1576
  Dihedral  :  5.240  70.230   1262
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 21.40 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.71 (0.25), residues: 1150
  helix:  1.85 (0.25), residues: 412
  sheet: -0.42 (0.29), residues: 294
  loop : -0.07 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 339 
 HIS   0.003   0.001   HIS D 210 
 PHE   0.029   0.002   PHE A  55 
 TYR   0.016   0.001   TYR D 179 
 ARG   0.008   0.000   ARG A  38 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 246
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8508 (p) cc_final: 0.8212 (p)
REVERT: A    9 ASP cc_start: 0.7871 (m-30) cc_final: 0.7605 (m-30)
REVERT: A   39 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7157 (mt-10)
REVERT: A  201 PHE cc_start: 0.8544 (m-80) cc_final: 0.7648 (m-80)
REVERT: A  236 ASP cc_start: 0.7424 (t0) cc_final: 0.7221 (t0)
REVERT: A  290 ASP cc_start: 0.7728 (m-30) cc_final: 0.7397 (m-30)
REVERT: A  307 GLU cc_start: 0.8022 (tp30) cc_final: 0.7706 (tp30)
REVERT: A  322 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7828 (ttmm)
REVERT: A  341 PHE cc_start: 0.8570 (t80) cc_final: 0.8029 (t80)
REVERT: B   52 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7236 (mtt90)
REVERT: B   87 THR cc_start: 0.8232 (m) cc_final: 0.7912 (t)
REVERT: B   98 SER cc_start: 0.8105 (p) cc_final: 0.7737 (t)
REVERT: B  212 ASP cc_start: 0.7726 (t70) cc_final: 0.7478 (t0)
REVERT: B  258 ASP cc_start: 0.7603 (m-30) cc_final: 0.7225 (t0)
REVERT: B  271 CYS cc_start: 0.8012 (m) cc_final: 0.7708 (p)
REVERT: B  312 ASP cc_start: 0.7597 (t0) cc_final: 0.7338 (t70)
REVERT: D   74 THR cc_start: 0.8067 (t) cc_final: 0.7773 (p)
REVERT: D   75 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7823 (t)
REVERT: D  202 ASN cc_start: 0.8221 (p0) cc_final: 0.8015 (p0)
REVERT: D  323 PHE cc_start: 0.8606 (m-80) cc_final: 0.8142 (m-80)
REVERT: D  329 ILE cc_start: 0.8426 (tp) cc_final: 0.8212 (tt)
REVERT: D  336 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7941 (ttt180)
REVERT: H   30 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8176 (t)
REVERT: H   63 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8198 (t)
REVERT: H  145 SER cc_start: 0.7826 (t) cc_final: 0.7615 (t)
  outliers start: 38
  outliers final: 23
  residues processed: 262
  average time/residue: 1.1315
  time to fit residues: 317.3302
Evaluate side-chains
  266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 239
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  336 ARG
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0970
   chunk 111 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0010
   chunk 27 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.5784

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.129584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115575 restraints weight = 12086.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.89
r_work: 0.3338 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9196  Z= 0.222
  Angle     :  0.581   9.276  12484  Z= 0.297
  Chirality :  0.043   0.185   1437
  Planarity :  0.004   0.041   1576
  Dihedral  :  5.189  69.933   1262
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 22.44 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.70 (0.25), residues: 1150
  helix:  1.86 (0.25), residues: 413
  sheet: -0.40 (0.29), residues: 297
  loop : -0.12 (0.32), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 216 
 HIS   0.003   0.001   HIS D 210 
 PHE   0.035   0.002   PHE A  55 
 TYR   0.017   0.001   TYR D 179 
 ARG   0.008   0.001   ARG A  38 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 239
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8523 (p) cc_final: 0.8244 (p)
REVERT: A    9 ASP cc_start: 0.7897 (m-30) cc_final: 0.7650 (m-30)
REVERT: A   10 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8189 (mtmm)
REVERT: A   39 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7156 (mt-10)
REVERT: A  201 PHE cc_start: 0.8553 (m-80) cc_final: 0.7636 (m-80)
REVERT: A  290 ASP cc_start: 0.7727 (m-30) cc_final: 0.7406 (m-30)
REVERT: A  307 GLU cc_start: 0.8057 (tp30) cc_final: 0.7738 (tp30)
REVERT: A  322 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7827 (ttmm)
REVERT: A  341 PHE cc_start: 0.8564 (t80) cc_final: 0.8031 (t80)
REVERT: B   52 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7368 (mtt90)
REVERT: B   98 SER cc_start: 0.8187 (p) cc_final: 0.7831 (t)
REVERT: B  212 ASP cc_start: 0.7726 (t70) cc_final: 0.7480 (t0)
REVERT: B  221 THR cc_start: 0.8305 (t) cc_final: 0.8076 (m)
REVERT: B  227 SER cc_start: 0.8549 (m) cc_final: 0.8034 (t)
REVERT: B  271 CYS cc_start: 0.8023 (m) cc_final: 0.7727 (p)
REVERT: B  312 ASP cc_start: 0.7605 (t0) cc_final: 0.7330 (t70)
REVERT: D   74 THR cc_start: 0.8043 (t) cc_final: 0.7744 (p)
REVERT: D   75 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7822 (t)
REVERT: D  115 LYS cc_start: 0.8470 (mtpt) cc_final: 0.7613 (mtpt)
REVERT: D  202 ASN cc_start: 0.8247 (p0) cc_final: 0.8044 (p0)
REVERT: D  213 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8035 (mp)
REVERT: D  305 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7631 (tm)
REVERT: D  323 PHE cc_start: 0.8601 (m-80) cc_final: 0.8114 (m-80)
REVERT: D  329 ILE cc_start: 0.8419 (tp) cc_final: 0.8201 (tt)
REVERT: H   30 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8176 (t)
REVERT: H   63 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8093 (t)
REVERT: H  145 SER cc_start: 0.7811 (t) cc_final: 0.7608 (t)
  outliers start: 37
  outliers final: 24
  residues processed: 254
  average time/residue: 1.1702
  time to fit residues: 318.0107
Evaluate side-chains
  266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 237
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  145 LYS
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  213 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   63 THR
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0570
   chunk 88 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.129251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.115194 restraints weight = 12085.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.89
r_work: 0.3344 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9196  Z= 0.228
  Angle     :  0.588   8.741  12484  Z= 0.300
  Chirality :  0.043   0.209   1437
  Planarity :  0.004   0.040   1576
  Dihedral  :  5.130  69.673   1262
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.28 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.72 (0.25), residues: 1150
  helix:  1.89 (0.25), residues: 412
  sheet: -0.36 (0.29), residues: 291
  loop : -0.16 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 339 
 HIS   0.003   0.001   HIS D 210 
 PHE   0.049   0.002   PHE A  55 
 TYR   0.020   0.002   TYR D 237 
 ARG   0.009   0.001   ARG A  38 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 240
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 SER cc_start: 0.8516 (p) cc_final: 0.8240 (p)
REVERT: A    9 ASP cc_start: 0.7879 (m-30) cc_final: 0.7652 (m-30)
REVERT: A   10 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8182 (mtmm)
REVERT: A   39 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7201 (mt-10)
REVERT: A  201 PHE cc_start: 0.8553 (m-80) cc_final: 0.7725 (m-80)
REVERT: A  290 ASP cc_start: 0.7750 (m-30) cc_final: 0.7431 (m-30)
REVERT: A  307 GLU cc_start: 0.8072 (tp30) cc_final: 0.7749 (tp30)
REVERT: A  322 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7767 (ttmm)
REVERT: B   52 ARG cc_start: 0.7703 (ttm-80) cc_final: 0.7371 (mtt90)
REVERT: B   98 SER cc_start: 0.8160 (p) cc_final: 0.7841 (t)
REVERT: B  212 ASP cc_start: 0.7709 (t70) cc_final: 0.7475 (t0)
REVERT: B  221 THR cc_start: 0.8284 (t) cc_final: 0.8067 (m)
REVERT: B  227 SER cc_start: 0.8550 (m) cc_final: 0.8001 (t)
REVERT: B  246 ASP cc_start: 0.7784 (m-30) cc_final: 0.7458 (m-30)
REVERT: B  271 CYS cc_start: 0.7992 (m) cc_final: 0.7710 (p)
REVERT: B  312 ASP cc_start: 0.7600 (t0) cc_final: 0.7319 (t70)
REVERT: D   44 GLN cc_start: 0.8155 (tt0) cc_final: 0.7933 (tp40)
REVERT: D   74 THR cc_start: 0.7986 (t) cc_final: 0.7688 (p)
REVERT: D   75 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7812 (t)
REVERT: D  115 LYS cc_start: 0.8444 (mtpt) cc_final: 0.7640 (mtpt)
REVERT: D  126 SER cc_start: 0.8637 (t) cc_final: 0.8417 (m)
REVERT: D  305 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7615 (tm)
REVERT: D  323 PHE cc_start: 0.8609 (m-80) cc_final: 0.8137 (m-80)
REVERT: D  329 ILE cc_start: 0.8410 (tp) cc_final: 0.8193 (tt)
REVERT: H   30 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8181 (t)
REVERT: H   67 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7695 (ttp80)
REVERT: H  145 SER cc_start: 0.7793 (t) cc_final: 0.7590 (t)
  outliers start: 30
  outliers final: 23
  residues processed: 254
  average time/residue: 1.1662
  time to fit residues: 316.9787
Evaluate side-chains
  262 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 236
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue   52 LYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain D residue   75 VAL
Chi-restraints excluded: chain D residue  154 THR
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  296 ILE
Chi-restraints excluded: chain D residue  305 LEU
Chi-restraints excluded: chain D residue  350 THR
Chi-restraints excluded: chain D residue  365 VAL
Chi-restraints excluded: chain G residue   54 VAL
Chi-restraints excluded: chain H residue   30 SER
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue  155 VAL
Chi-restraints excluded: chain H residue  199 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 57 optimal weight:    0.4980
   chunk 86 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 12 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.129197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.115184 restraints weight = 12068.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.88
r_work: 0.3347 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.4075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9196  Z= 0.223
  Angle     :  0.591   9.079  12484  Z= 0.301
  Chirality :  0.043   0.190   1437
  Planarity :  0.004   0.039   1576
  Dihedral  :  5.081  69.407   1262
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 23.80 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  0.71 (0.25), residues: 1150
  helix:  1.90 (0.25), residues: 412
  sheet: -0.39 (0.29), residues: 293
  loop : -0.16 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 216 
 HIS   0.003   0.001   HIS D 210 
 PHE   0.048   0.002   PHE A  55 
 TYR   0.023   0.002   TYR D 237 
 ARG   0.009   0.001   ARG A  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8079.65 seconds
wall clock time: 142 minutes 55.19 seconds (8575.19 seconds total)