Starting phenix.real_space_refine
on Mon Jul 28 02:19:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wun_21917/07_2025/6wun_21917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wun_21917/07_2025/6wun_21917.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wun_21917/07_2025/6wun_21917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wun_21917/07_2025/6wun_21917.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wun_21917/07_2025/6wun_21917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wun_21917/07_2025/6wun_21917.cif"
  }
  resolution = 3.9
  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=   0.023 sd=   0.112
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      16      5.16       5
     C    6370      2.51       5
     N    1814      2.21       5
     O    1882      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10082
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2044
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 2044
          Classifications: {'peptide': 260}
          Link IDs: {'PTRANS': 21, 'TRANS': 238}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2997
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 2997
          Classifications: {'peptide': 403}
          Link IDs: {'PTRANS': 22, 'TRANS': 380}
          Chain breaks: 4
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 7.04, per 1000 atoms: 0.70
  Number of scatterers: 10082
  At special positions: 0
  Unit cell: (149.46, 121.9, 95.4, 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      16     16.00
     O    1882      8.00
     N    1814      7.00
     C    6370      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 2.91
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2404

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 14 sheets defined
      28.2% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 44
    Processing helix  chain 'A' and resid 57 through 62
      removed outlier: 3.605A  pdb=" N   ARG A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 82
      removed outlier: 4.888A  pdb=" N   TRP A  75 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 123
      removed outlier: 3.939A  pdb=" N   LEU A 123 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 163
      removed outlier: 3.799A  pdb=" N   LEU A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA A 158 " --> pdb=" O   GLN A 154 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 174
    Processing helix  chain 'A' and resid 175 through 177
      No H-bonds generated for 'chain 'A' and resid 175 through 177'
    Processing helix  chain 'A' and resid 178 through 187
      removed outlier: 3.636A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 178 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ARG A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 187 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 210
      removed outlier: 3.820A  pdb=" N   ALA A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ALA A 199 " --> pdb=" O   ALA A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 255
      removed outlier: 3.565A  pdb=" N   ALA A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASP A 248 " --> pdb=" O   ARG A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 280
      removed outlier: 3.538A  pdb=" N   ALA A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   TYR A 278 " --> pdb=" O   ALA A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 300 through 308
      removed outlier: 3.670A  pdb=" N   MET A 304 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   LYS A 306 " --> pdb=" O   GLY A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 321
      removed outlier: 3.548A  pdb=" N   ARG A 317 " --> pdb=" O   LEU A 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 71
      removed outlier: 4.585A  pdb=" N   ILE B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 86 through 97
      removed outlier: 4.193A  pdb=" N   ALA B  90 " --> pdb=" O   ARG B  86 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   PHE B  97 " --> pdb=" O   LYS B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 458
      removed outlier: 3.766A  pdb=" N   SER B 456 " --> pdb=" O   LYS B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 463
    Processing helix  chain 'C' and resid 38 through 44
    Processing helix  chain 'C' and resid 57 through 62
      removed outlier: 3.604A  pdb=" N   ARG C  62 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 82
      removed outlier: 4.889A  pdb=" N   TRP C  75 " --> pdb=" O   GLY C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 123
      removed outlier: 3.939A  pdb=" N   LEU C 123 " --> pdb=" O   ALA C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 163
      removed outlier: 3.799A  pdb=" N   LEU C 157 " --> pdb=" O   ALA C 153 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA C 158 " --> pdb=" O   GLN C 154 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU C 159 " --> pdb=" O   ALA C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 174
    Processing helix  chain 'C' and resid 175 through 177
      No H-bonds generated for 'chain 'C' and resid 175 through 177'
    Processing helix  chain 'C' and resid 178 through 187
      removed outlier: 3.636A  pdb=" N   LEU C 182 " --> pdb=" O   HIS C 178 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG C 183 " --> pdb=" O   ASP C 179 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU C 185 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL C 187 " --> pdb=" O   ARG C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 210
      removed outlier: 3.819A  pdb=" N   ALA C 198 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   ALA C 199 " --> pdb=" O   ALA C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 239 through 255
      removed outlier: 3.566A  pdb=" N   ALA C 246 " --> pdb=" O   SER C 242 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP C 248 " --> pdb=" O   ARG C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 280
      removed outlier: 3.539A  pdb=" N   ALA C 273 " --> pdb=" O   GLY C 269 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   TYR C 278 " --> pdb=" O   ALA C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 280 through 285
    Processing helix  chain 'C' and resid 300 through 308
      removed outlier: 3.671A  pdb=" N   MET C 304 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LYS C 306 " --> pdb=" O   GLY C 302 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 321
      removed outlier: 3.548A  pdb=" N   ARG C 317 " --> pdb=" O   LEU C 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 71
      removed outlier: 4.585A  pdb=" N   ILE D  65 " --> pdb=" O   LEU D  61 " (cutoff:3.500A)
      Proline residue:  D  68  - end of helix
    Processing helix  chain 'D' and resid 86 through 97
      removed outlier: 4.193A  pdb=" N   ALA D  90 " --> pdb=" O   ARG D  86 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   PHE D  97 " --> pdb=" O   LYS D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 446 through 458
      removed outlier: 3.765A  pdb=" N   SER D 456 " --> pdb=" O   LYS D 452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 458 through 463
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90
      removed outlier: 6.341A  pdb=" N   LEU A  52 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 105 " --> pdb=" O   THR A  51 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 139 through 141
      removed outlier: 3.643A  pdb=" N   VAL B 158 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER B 141 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ASN B 172 " --> pdb=" O   THR B 155 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL B 159 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR B 189 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE B 191 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   LEU B 197 " --> pdb=" O   ILE B 191 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 210
    Processing sheet with id=AA4, first strand: chain 'B' and resid 293 through 297
      removed outlier: 4.031A  pdb=" N   LEU B 339 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 396 through 397
      removed outlier: 3.715A  pdb=" N   ARG B 426 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 419
      removed outlier: 3.575A  pdb=" N   GLN B 419 " --> pdb=" O   GLY B 473 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483
    Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90
      removed outlier: 6.341A  pdb=" N   LEU C  52 " --> pdb=" O   LEU C  89 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU C 105 " --> pdb=" O   THR C  51 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 139 through 141
      removed outlier: 3.642A  pdb=" N   VAL D 158 " --> pdb=" O   VAL D 139 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER D 141 " --> pdb=" O   ASN D 156 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ASN D 172 " --> pdb=" O   THR D 155 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL D 159 " --> pdb=" O   THR D 168 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR D 189 " --> pdb=" O   LEU D 199 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE D 191 " --> pdb=" O   LEU D 197 " (cutoff:3.500A)
      removed outlier: 5.730A  pdb=" N   LEU D 197 " --> pdb=" O   ILE D 191 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 206 through 210
    Processing sheet with id=AB2, first strand: chain 'D' and resid 293 through 297
      removed outlier: 4.031A  pdb=" N   LEU D 339 " --> pdb=" O   ALA D 316 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 396 through 397
      removed outlier: 3.714A  pdb=" N   ARG D 426 " --> pdb=" O   ALA D 397 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 417 through 419
      removed outlier: 3.576A  pdb=" N   GLN D 419 " --> pdb=" O   GLY D 473 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 482 through 483

    244 hydrogen bonds defined for protein.
    672 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: 2.60

  Time building geometry restraints manager: 3.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3386
        1.34 -     1.46: 1864
        1.46 -     1.57: 5020
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 10298
  Sorted by residual:
  bond pdb=" C   PHE A  27 "
       pdb=" N   PRO A  28 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 2.34e-02 1.83e+03 3.02e+00
  bond pdb=" C   PHE C  27 "
       pdb=" N   PRO C  28 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.94e+00
  bond pdb=" C   SER D 255 "
       pdb=" N   PRO D 256 "
    ideal  model  delta    sigma   weight residual
    1.331  1.318  0.014 7.90e-03 1.60e+04 2.94e+00
  bond pdb=" C   SER B 255 "
       pdb=" N   PRO B 256 "
    ideal  model  delta    sigma   weight residual
    1.331  1.318  0.013 7.90e-03 1.60e+04 2.90e+00
  bond pdb=" CA  ALA B 182 "
       pdb=" C   ALA B 182 "
    ideal  model  delta    sigma   weight residual
    1.518  1.462  0.056 4.01e-02 6.22e+02 1.92e+00
  ... (remaining 10293 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 12798
        1.29 -     2.58: 938
        2.58 -     3.86: 174
        3.86 -     5.15: 54
        5.15 -     6.44: 20
  Bond angle restraints: 13984
  Sorted by residual:
  angle pdb=" N   VAL D 258 "
        pdb=" CA  VAL D 258 "
        pdb=" C   VAL D 258 "
      ideal   model   delta    sigma   weight residual
     112.98  108.27    4.71 1.25e+00 6.40e-01 1.42e+01
  angle pdb=" N   VAL B 258 "
        pdb=" CA  VAL B 258 "
        pdb=" C   VAL B 258 "
      ideal   model   delta    sigma   weight residual
     112.98  108.27    4.71 1.25e+00 6.40e-01 1.42e+01
  angle pdb=" N   GLU C  36 "
        pdb=" CA  GLU C  36 "
        pdb=" C   GLU C  36 "
      ideal   model   delta    sigma   weight residual
     111.02  115.67   -4.65 1.25e+00 6.40e-01 1.38e+01
  angle pdb=" N   GLU A  36 "
        pdb=" CA  GLU A  36 "
        pdb=" C   GLU A  36 "
      ideal   model   delta    sigma   weight residual
     111.02  115.64   -4.62 1.25e+00 6.40e-01 1.36e+01
  angle pdb=" N   VAL D 139 "
        pdb=" CA  VAL D 139 "
        pdb=" C   VAL D 139 "
      ideal   model   delta    sigma   weight residual
     108.82  105.18    3.64 1.22e+00 6.72e-01 8.88e+00
  ... (remaining 13979 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 5521
       17.13 -    34.26: 524
       34.26 -    51.39: 79
       51.39 -    68.53: 14
       68.53 -    85.66: 6
  Dihedral angle restraints: 6144
    sinusoidal: 2398
      harmonic: 3746
  Sorted by residual:
  dihedral pdb=" CA  PRO C  34 "
           pdb=" C   PRO C  34 "
           pdb=" N   ASN C  35 "
           pdb=" CA  ASN C  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.60  -31.40     0      5.00e+00 4.00e-02 3.94e+01
  dihedral pdb=" CA  PRO A  34 "
           pdb=" C   PRO A  34 "
           pdb=" N   ASN A  35 "
           pdb=" CA  ASN A  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.62  -31.38     0      5.00e+00 4.00e-02 3.94e+01
  dihedral pdb=" CA  LEU C 101 "
           pdb=" C   LEU C 101 "
           pdb=" N   PRO C 102 "
           pdb=" CA  PRO C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.26  -29.74     0      5.00e+00 4.00e-02 3.54e+01
  ... (remaining 6141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1156
       0.045 -    0.090: 310
       0.090 -    0.135: 90
       0.135 -    0.180: 12
       0.180 -    0.225: 2
  Chirality restraints: 1570
  Sorted by residual:
  chirality pdb=" CB  THR A  92 "
            pdb=" CA  THR A  92 "
            pdb=" OG1 THR A  92 "
            pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  THR C  92 "
            pdb=" CA  THR C  92 "
            pdb=" OG1 THR C  92 "
            pdb=" CG2 THR C  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  VAL D 139 "
            pdb=" N   VAL D 139 "
            pdb=" C   VAL D 139 "
            pdb=" CB  VAL D 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.14e-01
  ... (remaining 1567 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D 478 "   -0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO D 479 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO D 479 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 479 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 478 "   -0.037 5.00e-02 4.00e+02   5.68e-02 5.16e+00
        pdb=" N   PRO B 479 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 189 "   -0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO B 190 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 190 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 190 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 644
        2.71 -     3.26: 10480
        3.26 -     3.81: 14724
        3.81 -     4.35: 18561
        4.35 -     4.90: 31280
  Nonbonded interactions: 75689
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 419 "
            pdb=" OE1 GLU B 484 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" NE2 GLN D 419 "
            pdb=" OE1 GLU D 484 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" O   VAL A 283 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   VAL C 283 "
            pdb=" OG  SER C 287 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG  SER B 181 "
            pdb=" ND2 ASN B 184 "
     model   vdw
     2.187 3.120
  ... (remaining 75684 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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 group one per residue
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:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.400
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
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      :  0.005   0.056  10298  Z= 0.226
  Angle     :  0.804   6.441  13984  Z= 0.447
  Chirality :  0.046   0.225   1570
  Planarity :  0.005   0.057   1828
  Dihedral  : 13.701  85.657   3740
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.40 %
    Favored  : 81.60 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  4.36 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -6.35 (0.17), residues: 1288
  helix: -3.60 (0.19), residues: 342
  sheet: -4.96 (0.21), residues: 320
  loop : -4.12 (0.19), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 244 
 HIS   0.003   0.001   HIS C 178 
 PHE   0.017   0.002   PHE B 396 
 TYR   0.014   0.001   TYR D 289 
 ARG   0.006   0.000   ARG A 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28351 (  244)
  hydrogen bonds       : angle       9.96786 (  672)
  covalent geometry    : bond        0.00486 (10298)
  covalent geometry    : angle       0.80408 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
REVERT: B  180 ARG cc_start: 0.6806 (ptp90) cc_final: 0.6391 (ptp90)
REVERT: B  184 ASN cc_start: 0.7799 (m-40) cc_final: 0.6882 (t0)
REVERT: B  283 MET cc_start: 0.8719 (mmt) cc_final: 0.8210 (mmt)
REVERT: B  389 ASP cc_start: 0.8198 (t0) cc_final: 0.7925 (t0)
REVERT: B  484 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7519 (mm-30)
REVERT: C   43 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8649 (tp40)
REVERT: D  180 ARG cc_start: 0.6930 (ptp90) cc_final: 0.6651 (ptp90)
REVERT: D  184 ASN cc_start: 0.7863 (m-40) cc_final: 0.7085 (t0)
REVERT: D  257 THR cc_start: 0.8739 (m) cc_final: 0.8428 (m)
REVERT: D  283 MET cc_start: 0.8754 (mmt) cc_final: 0.7980 (mmt)
REVERT: D  419 GLN cc_start: 0.6216 (tt0) cc_final: 0.5535 (tt0)
REVERT: D  484 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7311 (mm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 143
  average time/residue: 0.2295
  time to fit residues: 46.2050
Evaluate side-chains
  101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain C residue   92 THR
Chi-restraints excluded: chain D residue  255 SER
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  354 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
B  64 GLN
B 367 GLN
C  76 GLN
D  64 GLN
D 215 HIS
D 367 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.143656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.126212 restraints weight = 15615.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.126064 restraints weight = 28619.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127141 restraints weight = 22814.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10298  Z= 0.161
  Angle     :  0.744   8.269  13984  Z= 0.372
  Chirality :  0.045   0.160   1570
  Planarity :  0.005   0.047   1828
  Dihedral  :  6.584  43.307   1451
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.90 %
    Favored  : 86.10 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  8.90 %
    Favored  : 90.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.33 %

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: -5.21 (0.20), residues: 1288
  helix: -1.98 (0.25), residues: 344
  sheet: -4.58 (0.22), residues: 300
  loop : -3.75 (0.21), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 168 
 HIS   0.003   0.001   HIS A 178 
 PHE   0.020   0.002   PHE D 140 
 TYR   0.011   0.001   TYR D 240 
 ARG   0.003   0.000   ARG A  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04926 (  244)
  hydrogen bonds       : angle       5.77272 (  672)
  covalent geometry    : bond        0.00352 (10298)
  covalent geometry    : angle       0.74404 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  209 GLN cc_start: 0.7875 (tp40) cc_final: 0.7394 (tp40)
REVERT: B  216 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6864 (mt-10)
REVERT: B  283 MET cc_start: 0.8651 (mmt) cc_final: 0.8225 (mmt)
REVERT: B  389 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7740 (t0)
REVERT: D  180 ARG cc_start: 0.6745 (ptp90) cc_final: 0.6417 (ttp80)
REVERT: D  283 MET cc_start: 0.8701 (mmt) cc_final: 0.8050 (mmt)
REVERT: D  476 TYR cc_start: 0.8209 (t80) cc_final: 0.7991 (t80)
REVERT: D  486 ASN cc_start: 0.7515 (m-40) cc_final: 0.6896 (m-40)
  outliers start: 9
  outliers final: 8
  residues processed: 111
  average time/residue: 0.2125
  time to fit residues: 34.9148
Evaluate side-chains
  95 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  271 THR
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  354 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 81 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0060
   chunk 13 optimal weight:    8.9990
   chunk 30 optimal weight:    4.9990
   chunk 127 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 101 optimal weight:    0.1980
   chunk 31 optimal weight:    8.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
B 419 GLN
D 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.130594 restraints weight = 15559.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.130743 restraints weight = 26510.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131031 restraints weight = 22911.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10298  Z= 0.120
  Angle     :  0.658   7.964  13984  Z= 0.329
  Chirality :  0.043   0.150   1570
  Planarity :  0.005   0.041   1828
  Dihedral  :  5.971  34.485   1448
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.64 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.46 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -4.45 (0.21), residues: 1288
  helix: -0.94 (0.28), residues: 332
  sheet: -4.28 (0.23), residues: 310
  loop : -3.38 (0.22), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.024   0.002   PHE A 126 
 TYR   0.007   0.001   TYR D 240 
 ARG   0.004   0.000   ARG B 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (  244)
  hydrogen bonds       : angle       4.88245 (  672)
  covalent geometry    : bond        0.00259 (10298)
  covalent geometry    : angle       0.65768 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 1.107 
Fit side-chains
REVERT: B  209 GLN cc_start: 0.7745 (tp40) cc_final: 0.7371 (tp40)
REVERT: B  283 MET cc_start: 0.8613 (mmt) cc_final: 0.8153 (mmt)
REVERT: D  180 ARG cc_start: 0.6568 (ptp90) cc_final: 0.6162 (ttp80)
REVERT: D  283 MET cc_start: 0.8680 (mmt) cc_final: 0.7929 (mmt)
REVERT: D  476 TYR cc_start: 0.8170 (t80) cc_final: 0.7963 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 107
  average time/residue: 0.1857
  time to fit residues: 30.5828
Evaluate side-chains
  97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain C residue  304 MET
Chi-restraints excluded: chain C residue  310 ASN
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  354 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 123 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 56 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 101 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 184 ASN
B 419 GLN
D 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.147281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.129748 restraints weight = 15535.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.129354 restraints weight = 27749.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.129841 restraints weight = 23974.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10298  Z= 0.127
  Angle     :  0.656   8.889  13984  Z= 0.325
  Chirality :  0.043   0.147   1570
  Planarity :  0.004   0.040   1828
  Dihedral  :  5.786  34.482   1448
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.89 %
    Favored  : 87.11 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.84 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -4.13 (0.22), residues: 1288
  helix: -0.53 (0.29), residues: 334
  sheet: -4.03 (0.25), residues: 298
  loop : -3.34 (0.22), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 215 
 PHE   0.024   0.002   PHE C 126 
 TYR   0.009   0.001   TYR A 186 
 ARG   0.003   0.000   ARG B 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03254 (  244)
  hydrogen bonds       : angle       4.54358 (  672)
  covalent geometry    : bond        0.00289 (10298)
  covalent geometry    : angle       0.65617 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 GLN cc_start: 0.8542 (tp40) cc_final: 0.7762 (tm-30)
REVERT: B  485 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8253 (mt)
REVERT: C   27 PHE cc_start: 0.6118 (t80) cc_final: 0.5822 (t80)
REVERT: D  180 ARG cc_start: 0.6623 (ptp90) cc_final: 0.6336 (ttp80)
REVERT: D  216 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7453 (mt-10)
REVERT: D  283 MET cc_start: 0.8681 (mmt) cc_final: 0.7793 (mmt)
  outliers start: 27
  outliers final: 17
  residues processed: 111
  average time/residue: 0.2215
  time to fit residues: 38.1298
Evaluate side-chains
  98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 1.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  333 VAL
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  310 ASN
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  312 THR
Chi-restraints excluded: chain D residue  333 VAL
Chi-restraints excluded: chain D residue  354 THR
Chi-restraints excluded: chain D residue  458 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 127 optimal weight:    8.9990
   chunk 91 optimal weight:    0.0870
   chunk 126 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:   20.0000
   chunk 125 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 112 optimal weight:    7.9990
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
B 367 GLN
D 367 GLN
D 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.147879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.129933 restraints weight = 15579.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128877 restraints weight = 25939.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.129809 restraints weight = 25809.548|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10298  Z= 0.126
  Angle     :  0.667   9.708  13984  Z= 0.328
  Chirality :  0.042   0.148   1570
  Planarity :  0.004   0.037   1828
  Dihedral  :  5.713  34.339   1448
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.03 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.16 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.88 (0.22), residues: 1288
  helix: -0.29 (0.29), residues: 334
  sheet: -3.79 (0.26), residues: 296
  loop : -3.27 (0.22), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.020   0.002   PHE B 100 
 TYR   0.016   0.001   TYR B 421 
 ARG   0.002   0.000   ARG B 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03143 (  244)
  hydrogen bonds       : angle       4.39053 (  672)
  covalent geometry    : bond        0.00286 (10298)
  covalent geometry    : angle       0.66733 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.954 
Fit side-chains
REVERT: B  209 GLN cc_start: 0.8171 (tp40) cc_final: 0.7632 (mm-40)
REVERT: B  283 MET cc_start: 0.8727 (mmt) cc_final: 0.7613 (mmt)
REVERT: B  485 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8249 (mt)
REVERT: C   27 PHE cc_start: 0.6150 (t80) cc_final: 0.5873 (t80)
REVERT: C  306 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7756 (mtmm)
REVERT: D  180 ARG cc_start: 0.6603 (ptp90) cc_final: 0.6219 (ttp80)
REVERT: D  209 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7930 (mm110)
REVERT: D  216 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7522 (mt-10)
REVERT: D  283 MET cc_start: 0.8538 (mmt) cc_final: 0.7615 (mmt)
REVERT: D  420 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7727 (pp)
REVERT: D  476 TYR cc_start: 0.8457 (t80) cc_final: 0.8102 (t80)
  outliers start: 22
  outliers final: 13
  residues processed: 104
  average time/residue: 0.3144
  time to fit residues: 50.5003
Evaluate side-chains
  99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 1.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  485 LEU
Chi-restraints excluded: chain C residue  310 ASN
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  271 THR
Chi-restraints excluded: chain D residue  312 THR
Chi-restraints excluded: chain D residue  354 THR
Chi-restraints excluded: chain D residue  420 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 49 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 115 optimal weight:    7.9990
   chunk 43 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 89 optimal weight:    9.9990
   chunk 13 optimal weight:    0.2980
   chunk 54 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 367 GLN
D 367 GLN
D 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.148028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.130812 restraints weight = 15663.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.130991 restraints weight = 27235.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131650 restraints weight = 23893.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10298  Z= 0.125
  Angle     :  0.653   9.134  13984  Z= 0.321
  Chirality :  0.042   0.150   1570
  Planarity :  0.004   0.037   1828
  Dihedral  :  5.546  33.993   1446
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.20 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.73 %
    Favored  : 84.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.76 (0.22), residues: 1288
  helix: -0.10 (0.29), residues: 334
  sheet: -3.76 (0.25), residues: 306
  loop : -3.21 (0.22), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 168 
 HIS   0.003   0.001   HIS B 215 
 PHE   0.023   0.001   PHE D  66 
 TYR   0.009   0.001   TYR B 421 
 ARG   0.002   0.000   ARG D 494 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02887 (  244)
  hydrogen bonds       : angle       4.25517 (  672)
  covalent geometry    : bond        0.00287 (10298)
  covalent geometry    : angle       0.65269 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 1.173 
Fit side-chains
REVERT: A  211 GLN cc_start: 0.8571 (tp40) cc_final: 0.7741 (tm-30)
REVERT: B  283 MET cc_start: 0.8689 (mmt) cc_final: 0.7547 (mmt)
REVERT: B  420 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7667 (pp)
REVERT: C   27 PHE cc_start: 0.6178 (t80) cc_final: 0.5884 (t80)
REVERT: D  180 ARG cc_start: 0.6630 (ptp90) cc_final: 0.6238 (ttp80)
REVERT: D  209 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8005 (mm-40)
REVERT: D  283 MET cc_start: 0.8489 (mmt) cc_final: 0.7524 (mmt)
REVERT: D  420 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7718 (pp)
REVERT: D  476 TYR cc_start: 0.8327 (t80) cc_final: 0.8006 (t80)
  outliers start: 23
  outliers final: 14
  residues processed: 107
  average time/residue: 0.1730
  time to fit residues: 28.7752
Evaluate side-chains
  99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  310 ASN
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  271 THR
Chi-restraints excluded: chain D residue  312 THR
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  458 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   chunk 76 optimal weight:    0.0770
   chunk 25 optimal weight:    0.2980
   chunk 108 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.8744

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
B 367 GLN
** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 367 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.146577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128561 restraints weight = 15860.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.127247 restraints weight = 23367.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128456 restraints weight = 20352.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10298  Z= 0.146
  Angle     :  0.679   9.647  13984  Z= 0.334
  Chirality :  0.043   0.196   1570
  Planarity :  0.004   0.038   1828
  Dihedral  :  5.612  33.768   1444
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.51 %
    Favored  : 86.49 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.96 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.81 (0.22), residues: 1288
  helix: -0.04 (0.29), residues: 334
  sheet: -4.01 (0.23), residues: 350
  loop : -3.00 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS C 202 
 PHE   0.028   0.002   PHE D  66 
 TYR   0.016   0.001   TYR B 421 
 ARG   0.002   0.000   ARG D 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (  244)
  hydrogen bonds       : angle       4.30977 (  672)
  covalent geometry    : bond        0.00339 (10298)
  covalent geometry    : angle       0.67925 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.035 
Fit side-chains
REVERT: A  211 GLN cc_start: 0.8531 (tp40) cc_final: 0.7651 (tm-30)
REVERT: B  283 MET cc_start: 0.8715 (mmt) cc_final: 0.7522 (mmt)
REVERT: B  420 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7641 (pp)
REVERT: C   27 PHE cc_start: 0.6313 (t80) cc_final: 0.5964 (t80)
REVERT: C  304 MET cc_start: 0.7834 (ptm) cc_final: 0.7501 (ptm)
REVERT: D  180 ARG cc_start: 0.6619 (ptp90) cc_final: 0.6247 (ttp80)
REVERT: D  209 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7996 (mm110)
REVERT: D  283 MET cc_start: 0.8371 (mmt) cc_final: 0.7377 (mmt)
REVERT: D  420 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7702 (pp)
REVERT: D  476 TYR cc_start: 0.8375 (t80) cc_final: 0.8079 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 102
  average time/residue: 0.1808
  time to fit residues: 28.6845
Evaluate side-chains
  99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain C residue  310 ASN
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  271 THR
Chi-restraints excluded: chain D residue  312 THR
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  458 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 67 optimal weight:    0.0040
   chunk 100 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 130 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    1.6796

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

Flipped N/Q/H residues before XYZ refinement:
B 367 GLN
D 367 GLN
** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.147021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.127987 restraints weight = 15640.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.126336 restraints weight = 23706.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.127184 restraints weight = 25995.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10298  Z= 0.137
  Angle     :  0.672   9.800  13984  Z= 0.329
  Chirality :  0.042   0.171   1570
  Planarity :  0.004   0.039   1828
  Dihedral  :  5.590  33.963   1444
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.81 %
    Favored  : 87.19 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.96 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.69 (0.23), residues: 1288
  helix:  0.00 (0.29), residues: 348
  sheet: -3.79 (0.24), residues: 318
  loop : -3.18 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A 202 
 PHE   0.021   0.002   PHE D  66 
 TYR   0.011   0.001   TYR D 421 
 ARG   0.002   0.000   ARG D 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02963 (  244)
  hydrogen bonds       : angle       4.25347 (  672)
  covalent geometry    : bond        0.00319 (10298)
  covalent geometry    : angle       0.67168 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 1.080 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: A  211 GLN cc_start: 0.8461 (tp40) cc_final: 0.7691 (tm-30)
REVERT: B  283 MET cc_start: 0.8695 (mmt) cc_final: 0.7520 (mmt)
REVERT: B  420 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7600 (pp)
REVERT: C   27 PHE cc_start: 0.6438 (t80) cc_final: 0.6086 (t80)
REVERT: C  304 MET cc_start: 0.7883 (ptm) cc_final: 0.7415 (ptm)
REVERT: D  180 ARG cc_start: 0.6668 (ptp90) cc_final: 0.6235 (ttp80)
REVERT: D  283 MET cc_start: 0.8283 (mmt) cc_final: 0.7351 (mmt)
REVERT: D  420 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7718 (pp)
REVERT: D  476 TYR cc_start: 0.8377 (t80) cc_final: 0.8145 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 99
  average time/residue: 0.1761
  time to fit residues: 27.2079
Evaluate side-chains
  97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  271 THR
Chi-restraints excluded: chain D residue  312 THR
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  458 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   chunk 127 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9980
   chunk 114 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
B 367 GLN
D 367 GLN
** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.146760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129041 restraints weight = 15668.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.129776 restraints weight = 30712.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130702 restraints weight = 20496.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10298  Z= 0.144
  Angle     :  0.682   9.353  13984  Z= 0.334
  Chirality :  0.042   0.158   1570
  Planarity :  0.004   0.039   1828
  Dihedral  :  5.583  33.754   1444
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.66 %
    Favored  : 86.34 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.34 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.69 (0.23), residues: 1288
  helix:  0.07 (0.29), residues: 334
  sheet: -3.95 (0.23), residues: 350
  loop : -2.94 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.027   0.002   PHE B 100 
 TYR   0.009   0.001   TYR D 421 
 ARG   0.004   0.000   ARG C 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02912 (  244)
  hydrogen bonds       : angle       4.25855 (  672)
  covalent geometry    : bond        0.00336 (10298)
  covalent geometry    : angle       0.68153 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.092 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7989 (mp)
REVERT: A  211 GLN cc_start: 0.8415 (tp40) cc_final: 0.7637 (tm-30)
REVERT: B  283 MET cc_start: 0.8705 (mmt) cc_final: 0.7471 (mmt)
REVERT: B  420 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7597 (pp)
REVERT: C   27 PHE cc_start: 0.6288 (t80) cc_final: 0.6032 (t80)
REVERT: D  180 ARG cc_start: 0.6592 (ptp90) cc_final: 0.6238 (ttp80)
REVERT: D  283 MET cc_start: 0.8208 (mmt) cc_final: 0.7290 (mmt)
REVERT: D  420 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7682 (pp)
REVERT: D  476 TYR cc_start: 0.8361 (t80) cc_final: 0.8101 (t80)
  outliers start: 19
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1763
  time to fit residues: 28.6305
Evaluate side-chains
  101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  271 THR
Chi-restraints excluded: chain D residue  312 THR
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  458 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 78 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 103 optimal weight:    0.8980
   chunk 128 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 96 optimal weight:    9.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 419 GLN
D 367 GLN
D 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.147375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129337 restraints weight = 15631.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128312 restraints weight = 25591.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.129384 restraints weight = 22382.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10298  Z= 0.138
  Angle     :  0.680   9.243  13984  Z= 0.335
  Chirality :  0.042   0.159   1570
  Planarity :  0.004   0.040   1828
  Dihedral  :  5.556  33.608   1444
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.66 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.34 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.62 (0.23), residues: 1288
  helix:  0.10 (0.30), residues: 334
  sheet: -3.87 (0.23), residues: 352
  loop : -2.89 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 328 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.014   0.001   PHE A  27 
 TYR   0.011   0.001   TYR D 421 
 ARG   0.006   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02812 (  244)
  hydrogen bonds       : angle       4.21986 (  672)
  covalent geometry    : bond        0.00322 (10298)
  covalent geometry    : angle       0.68003 (13984)

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

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

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2576 Ramachandran restraints generated.
    1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A   37 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7985 (mp)
REVERT: A  211 GLN cc_start: 0.8429 (tp40) cc_final: 0.7728 (tm-30)
REVERT: B  283 MET cc_start: 0.8691 (mmt) cc_final: 0.7472 (mmt)
REVERT: B  420 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7587 (pp)
REVERT: C   27 PHE cc_start: 0.6297 (t80) cc_final: 0.6029 (t80)
REVERT: D  180 ARG cc_start: 0.6659 (ptp90) cc_final: 0.6265 (ttp80)
REVERT: D  283 MET cc_start: 0.8193 (mmt) cc_final: 0.7350 (mmt)
REVERT: D  420 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7601 (pp)
REVERT: D  476 TYR cc_start: 0.8363 (t80) cc_final: 0.8100 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 96
  average time/residue: 0.1681
  time to fit residues: 25.4927
Evaluate side-chains
  96 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  271 THR
Chi-restraints excluded: chain D residue  312 THR
Chi-restraints excluded: chain D residue  420 LEU
Chi-restraints excluded: chain D residue  458 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 93 optimal weight:   20.0000
   chunk 52 optimal weight:    0.0770
   chunk 32 optimal weight:    0.3980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 125 optimal weight:    0.8980
   chunk 111 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   chunk 58 optimal weight:    0.9980
   chunk 124 optimal weight:    6.9990
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B 419 GLN
B 423 ASN
D 367 GLN
D 419 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.151497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.134540 restraints weight = 15464.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133444 restraints weight = 22152.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.134563 restraints weight = 20880.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10298  Z= 0.106
  Angle     :  0.651   9.072  13984  Z= 0.318
  Chirality :  0.041   0.154   1570
  Planarity :  0.004   0.035   1828
  Dihedral  :  5.224  33.488   1444
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 15.91 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.37 (0.23), residues: 1288
  helix:  0.26 (0.30), residues: 334
  sheet: -3.37 (0.27), residues: 284
  loop : -3.12 (0.22), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP C 328 
 HIS   0.004   0.001   HIS B 215 
 PHE   0.027   0.001   PHE D 100 
 TYR   0.009   0.001   TYR D 421 
 ARG   0.010   0.000   ARG C 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02533 (  244)
  hydrogen bonds       : angle       4.04940 (  672)
  covalent geometry    : bond        0.00236 (10298)
  covalent geometry    : angle       0.65127 (13984)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3120.59 seconds
wall clock time: 56 minutes 50.70 seconds (3410.70 seconds total)