Starting phenix.real_space_refine
on Sat Aug 23 05:15:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wun_21917/08_2025/6wun_21917.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wun_21917/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wun_21917/08_2025/6wun_21917.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wun_21917/08_2025/6wun_21917.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wun_21917/08_2025/6wun_21917.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wun_21917/08_2025/6wun_21917.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.05, per 1000 atoms: 0.30
  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: 1.10
  Conformation dependent library (CDL) restraints added in 433.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.35
  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: 1.25

  Time building geometry restraints manager: 1.42 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: 0.02
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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.590
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.070
-------------------------------------------------------------------------------
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 : 14.12
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.000   ARG A 108 
 TYR   0.014   0.001   TYR D 289 
 PHE   0.017   0.002   PHE B 396 
 TRP   0.008   0.001   TRP B 244 
 HIS   0.003   0.001   HIS C 178 

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

*********************** 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  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: B  180 ARG cc_start: 0.6806 (ptp90) cc_final: 0.6392 (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: 0.7312 (mm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 143
  average time/residue: 0.1115
  time to fit residues: 22.4229
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  : 0.435 
-------------------------------------------------------------------------------
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 98 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0970
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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
C  76 GLN
C 154 GLN
D  64 GLN
D 215 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.144063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.126299 restraints weight = 15793.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.126510 restraints weight = 29123.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.127469 restraints weight = 22529.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.127165 restraints weight = 16845.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.127702 restraints weight = 16243.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1507

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= 0.154
  Angle     :  0.739   7.909  13984  Z= 0.370
  Chirality :  0.045   0.164   1570
  Planarity :  0.005   0.047   1828
  Dihedral  :  6.569  43.461   1451
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.28 %
    Favored  : 86.72 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  9.00 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.16 (0.20), residues: 1288
  helix: -1.92 (0.26), residues: 332
  sheet: -4.55 (0.22), residues: 294
  loop : -3.72 (0.21), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  80 
 TYR   0.010   0.001   TYR D 240 
 PHE   0.019   0.002   PHE D 140 
 TRP   0.013   0.001   TRP A 168 
 HIS   0.002   0.001   HIS D 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10298)
  covalent geometry    : angle       0.73859 (13984)
  hydrogen bonds       : bond        0.05058 (  244)
  hydrogen bonds       : angle       5.82883 (  672)

*********************** 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
  115 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: B  180 ARG cc_start: 0.6451 (ptp90) cc_final: 0.6175 (mtp-110)
REVERT: B  209 GLN cc_start: 0.7919 (tp40) cc_final: 0.7613 (tp40)
REVERT: B  216 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6868 (mt-10)
REVERT: B  283 MET cc_start: 0.8622 (mmt) cc_final: 0.8218 (mmt)
REVERT: B  389 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7711 (t0)
REVERT: D  180 ARG cc_start: 0.6725 (ptp90) cc_final: 0.6169 (mtp180)
REVERT: D  257 THR cc_start: 0.8987 (m) cc_final: 0.8693 (m)
REVERT: D  283 MET cc_start: 0.8708 (mmt) cc_final: 0.8024 (mmt)
REVERT: D  476 TYR cc_start: 0.8209 (t80) cc_final: 0.7986 (t80)
REVERT: D  484 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7818 (mm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 112
  average time/residue: 0.0974
  time to fit residues: 16.1705
Evaluate side-chains
  99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  138 LEU
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  389 ASP
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 101 optimal weight:    0.0770
   chunk 98 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 113 optimal weight:    0.9980
   chunk 66 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 125 optimal weight:    0.0570
   chunk 85 optimal weight:    9.9990
   overall best weight:    1.0058

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.130170 restraints weight = 15564.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.130534 restraints weight = 28405.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.131533 restraints weight = 21036.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.130999 restraints weight = 15406.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.131290 restraints weight = 14847.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10298  Z= 0.120
  Angle     :  0.666   8.558  13984  Z= 0.331
  Chirality :  0.043   0.149   1570
  Planarity :  0.005   0.041   1828
  Dihedral  :  5.988  34.307   1448
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.41 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.70 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.43 (0.21), residues: 1288
  helix: -0.92 (0.28), residues: 332
  sheet: -4.23 (0.23), residues: 310
  loop : -3.40 (0.22), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 375 
 TYR   0.008   0.001   TYR A 186 
 PHE   0.026   0.002   PHE A 126 
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (10298)
  covalent geometry    : angle       0.66561 (13984)
  hydrogen bonds       : bond        0.03787 (  244)
  hydrogen bonds       : angle       4.93142 (  672)

*********************** 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
  121 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: B  209 GLN cc_start: 0.7756 (tp40) cc_final: 0.7429 (tp40)
REVERT: B  283 MET cc_start: 0.8608 (mmt) cc_final: 0.8036 (mmt)
REVERT: B  389 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7602 (p0)
REVERT: C   42 GLN cc_start: 0.8745 (tp40) cc_final: 0.8525 (tp40)
REVERT: D  257 THR cc_start: 0.9029 (m) cc_final: 0.8740 (m)
REVERT: D  283 MET cc_start: 0.8628 (mmt) cc_final: 0.7942 (mmt)
REVERT: D  476 TYR cc_start: 0.8178 (t80) cc_final: 0.7958 (t80)
REVERT: D  486 ASN cc_start: 0.7430 (m-40) cc_final: 0.6800 (m-40)
  outliers start: 21
  outliers final: 11
  residues processed: 113
  average time/residue: 0.0822
  time to fit residues: 14.4881
Evaluate side-chains
  102 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
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  333 VAL
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain C residue  304 MET
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  354 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 100 optimal weight:   10.0000
   chunk 115 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 126 optimal weight:    0.7980
   chunk 128 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.3816 r_free = 0.3816 target = 0.143602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.123992 restraints weight = 15782.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.121811 restraints weight = 19589.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.122732 restraints weight = 23861.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.123608 restraints weight = 15699.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.124064 restraints weight = 13608.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10298  Z= 0.181
  Angle     :  0.712   8.840  13984  Z= 0.351
  Chirality :  0.044   0.150   1570
  Planarity :  0.005   0.043   1828
  Dihedral  :  6.097  33.918   1447
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.61 %
    Favored  : 84.39 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 11.55 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.33 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.28 (0.22), residues: 1288
  helix: -0.70 (0.28), residues: 334
  sheet: -4.24 (0.23), residues: 320
  loop : -3.27 (0.22), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 375 
 TYR   0.013   0.002   TYR B 289 
 PHE   0.023   0.002   PHE C 126 
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (10298)
  covalent geometry    : angle       0.71197 (13984)
  hydrogen bonds       : bond        0.03631 (  244)
  hydrogen bonds       : angle       4.83713 (  672)

*********************** 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
  122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.392 
Fit side-chains
REVERT: B  283 MET cc_start: 0.8717 (mmt) cc_final: 0.7900 (mmt)
REVERT: B  389 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7804 (t0)
REVERT: C   27 PHE cc_start: 0.6206 (t80) cc_final: 0.5892 (t80)
REVERT: D  283 MET cc_start: 0.8794 (mmt) cc_final: 0.7505 (mmt)
REVERT: D  420 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7641 (pp)
  outliers start: 27
  outliers final: 17
  residues processed: 114
  average time/residue: 0.0777
  time to fit residues: 13.9677
Evaluate side-chains
  105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
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  333 VAL
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  488 SER
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
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 36 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 127 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   overall best weight:    2.1388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.144542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.126530 restraints weight = 15791.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.126501 restraints weight = 31875.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.127198 restraints weight = 26874.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.127830 restraints weight = 17172.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128078 restraints weight = 15782.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10298  Z= 0.162
  Angle     :  0.703   8.674  13984  Z= 0.346
  Chirality :  0.043   0.148   1570
  Planarity :  0.004   0.042   1828
  Dihedral  :  6.015  33.881   1447
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.82 %
    Favored  : 86.18 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.16 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.17 (0.22), residues: 1288
  helix: -0.41 (0.29), residues: 332
  sheet: -4.26 (0.22), residues: 362
  loop : -3.10 (0.23), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 375 
 TYR   0.011   0.002   TYR B 289 
 PHE   0.024   0.002   PHE C 126 
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (10298)
  covalent geometry    : angle       0.70289 (13984)
  hydrogen bonds       : bond        0.03401 (  244)
  hydrogen bonds       : angle       4.65905 (  672)

*********************** 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
  109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 MET cc_start: 0.7247 (ttp) cc_final: 0.7025 (ttp)
REVERT: A  306 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7699 (mtmm)
REVERT: B  209 GLN cc_start: 0.8230 (tp40) cc_final: 0.7786 (mm-40)
REVERT: B  389 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7692 (t0)
REVERT: B  476 TYR cc_start: 0.8333 (t80) cc_final: 0.8114 (t80)
REVERT: C   27 PHE cc_start: 0.6332 (t80) cc_final: 0.6053 (t80)
REVERT: D  283 MET cc_start: 0.8749 (mmt) cc_final: 0.7409 (mmt)
  outliers start: 19
  outliers final: 15
  residues processed: 100
  average time/residue: 0.0803
  time to fit residues: 12.7149
Evaluate side-chains
  102 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
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  333 VAL
Chi-restraints excluded: chain B residue  354 THR
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  454 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  354 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 126 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 105 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.2584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.147413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.128940 restraints weight = 15743.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.128456 restraints weight = 28112.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.129518 restraints weight = 26097.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.129624 restraints weight = 16484.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.129861 restraints weight = 16464.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2711

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= 0.120
  Angle     :  0.663   9.297  13984  Z= 0.325
  Chirality :  0.042   0.148   1570
  Planarity :  0.004   0.033   1828
  Dihedral  :  5.715  33.671   1447
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.58 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 14.49 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.85 (0.22), residues: 1288
  helix: -0.18 (0.29), residues: 332
  sheet: -3.92 (0.24), residues: 316
  loop : -3.15 (0.23), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 375 
 TYR   0.020   0.001   TYR B 421 
 PHE   0.022   0.002   PHE C 126 
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10298)
  covalent geometry    : angle       0.66294 (13984)
  hydrogen bonds       : bond        0.03009 (  244)
  hydrogen bonds       : angle       4.40997 (  672)

*********************** 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
  109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 GLN cc_start: 0.8529 (tp40) cc_final: 0.7661 (tm-30)
REVERT: B  209 GLN cc_start: 0.8100 (tp40) cc_final: 0.7864 (mm-40)
REVERT: B  283 MET cc_start: 0.8608 (mmt) cc_final: 0.7526 (mmt)
REVERT: B  389 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7637 (t0)
REVERT: B  476 TYR cc_start: 0.8329 (t80) cc_final: 0.8091 (t80)
REVERT: C   27 PHE cc_start: 0.6259 (t80) cc_final: 0.5965 (t80)
REVERT: C  306 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7724 (mtmm)
REVERT: D  420 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7701 (pp)
  outliers start: 16
  outliers final: 13
  residues processed: 103
  average time/residue: 0.0777
  time to fit residues: 12.6855
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  : 0.396 
-------------------------------------------------------------------------------
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  354 THR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  458 VAL
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
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 3 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 90 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0770
   chunk 25 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   overall best weight:    2.3744

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.144158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.126921 restraints weight = 15719.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128034 restraints weight = 30065.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128429 restraints weight = 20818.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128188 restraints weight = 15600.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.128484 restraints weight = 14174.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10298  Z= 0.171
  Angle     :  0.704   9.388  13984  Z= 0.347
  Chirality :  0.043   0.148   1570
  Planarity :  0.004   0.032   1828
  Dihedral  :  5.875  33.637   1446
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.68 %
    Favored  : 84.32 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.25 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.93 (0.22), residues: 1288
  helix: -0.13 (0.29), residues: 334
  sheet: -4.14 (0.22), residues: 360
  loop : -3.00 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 205 
 TYR   0.015   0.002   TYR D 421 
 PHE   0.025   0.002   PHE D 100 
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS C 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (10298)
  covalent geometry    : angle       0.70449 (13984)
  hydrogen bonds       : bond        0.03202 (  244)
  hydrogen bonds       : angle       4.46735 (  672)

*********************** 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
  114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 GLN cc_start: 0.8531 (tp40) cc_final: 0.7572 (tm-30)
REVERT: B  209 GLN cc_start: 0.8122 (tp40) cc_final: 0.7917 (mm-40)
REVERT: B  283 MET cc_start: 0.8575 (mmt) cc_final: 0.7436 (mmt)
REVERT: B  389 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7696 (t0)
REVERT: B  476 TYR cc_start: 0.8346 (t80) cc_final: 0.8061 (t80)
REVERT: B  500 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6774 (ttt180)
REVERT: C   27 PHE cc_start: 0.6328 (t80) cc_final: 0.6006 (t80)
REVERT: C  304 MET cc_start: 0.7864 (ptm) cc_final: 0.7519 (ptm)
REVERT: D  420 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7615 (pp)
  outliers start: 23
  outliers final: 15
  residues processed: 106
  average time/residue: 0.0863
  time to fit residues: 13.6205
Evaluate side-chains
  102 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  354 THR
Chi-restraints excluded: chain B residue  389 ASP
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  500 ARG
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
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 24 optimal weight:    0.0670
   chunk 2 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 106 optimal weight:    0.7980
   chunk 29 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.149246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.131112 restraints weight = 15541.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130686 restraints weight = 24802.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.131905 restraints weight = 22158.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.132132 restraints weight = 14851.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.132551 restraints weight = 14005.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3024

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= 0.112
  Angle     :  0.667   9.257  13984  Z= 0.326
  Chirality :  0.042   0.211   1570
  Planarity :  0.004   0.037   1828
  Dihedral  :  5.510  33.599   1446
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.81 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.63 (0.23), residues: 1288
  helix:  0.04 (0.29), residues: 334
  sheet: -3.63 (0.26), residues: 294
  loop : -3.20 (0.22), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 245 
 TYR   0.012   0.001   TYR D 421 
 PHE   0.024   0.001   PHE C 126 
 TRP   0.007   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10298)
  covalent geometry    : angle       0.66690 (13984)
  hydrogen bonds       : bond        0.02942 (  244)
  hydrogen bonds       : angle       4.28635 (  672)

*********************** 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: 14
    poor density    : 90
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 GLN cc_start: 0.8499 (tp40) cc_final: 0.7593 (tm-30)
REVERT: B  209 GLN cc_start: 0.8183 (tp40) cc_final: 0.7808 (mm-40)
REVERT: B  283 MET cc_start: 0.8551 (mmt) cc_final: 0.7386 (mmt)
REVERT: B  389 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7544 (t0)
REVERT: B  476 TYR cc_start: 0.8283 (t80) cc_final: 0.7995 (t80)
REVERT: C   27 PHE cc_start: 0.6261 (t80) cc_final: 0.5908 (t80)
REVERT: D  420 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7715 (pp)
  outliers start: 14
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0806
  time to fit residues: 12.5117
Evaluate side-chains
  92 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  389 ASP
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  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 107 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0060
   chunk 20 optimal weight:    0.0970
   chunk 76 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0030
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.0208

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.149047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.130728 restraints weight = 15611.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.129701 restraints weight = 26442.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.130748 restraints weight = 25711.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131143 restraints weight = 15841.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.131438 restraints weight = 15492.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.3150

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= 0.115
  Angle     :  0.663   9.968  13984  Z= 0.323
  Chirality :  0.042   0.195   1570
  Planarity :  0.004   0.034   1828
  Dihedral  :  5.388  33.326   1444
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.49 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.48 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.51 (0.23), residues: 1288
  helix:  0.15 (0.30), residues: 334
  sheet: -3.55 (0.26), residues: 286
  loop : -3.16 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 205 
 TYR   0.007   0.001   TYR D 421 
 PHE   0.028   0.002   PHE B 100 
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10298)
  covalent geometry    : angle       0.66299 (13984)
  hydrogen bonds       : bond        0.02824 (  244)
  hydrogen bonds       : angle       4.19314 (  672)

*********************** 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
  97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 GLN cc_start: 0.8532 (tp40) cc_final: 0.7590 (tm-30)
REVERT: A  304 MET cc_start: 0.7763 (ptm) cc_final: 0.7344 (ptm)
REVERT: B  389 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7514 (t0)
REVERT: B  476 TYR cc_start: 0.8289 (t80) cc_final: 0.8039 (t80)
REVERT: C   27 PHE cc_start: 0.6327 (t80) cc_final: 0.6033 (t80)
REVERT: C  304 MET cc_start: 0.7802 (ptm) cc_final: 0.7343 (ptm)
REVERT: D  420 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7673 (pp)
  outliers start: 12
  outliers final: 9
  residues processed: 91
  average time/residue: 0.0819
  time to fit residues: 11.5504
Evaluate side-chains
  93 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  271 THR
Chi-restraints excluded: chain B residue  389 ASP
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  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 68 optimal weight:    7.9990
   chunk 104 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0770
   chunk 42 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    2.2144

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.145803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.127888 restraints weight = 15573.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.127654 restraints weight = 28305.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.128702 restraints weight = 23787.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.128736 restraints weight = 15944.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129104 restraints weight = 17834.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10298  Z= 0.165
  Angle     :  0.703  10.158  13984  Z= 0.343
  Chirality :  0.043   0.179   1570
  Planarity :  0.004   0.034   1828
  Dihedral  :  5.648  33.074   1444
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.21 %
    Favored  : 85.79 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.48 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.64 (0.23), residues: 1288
  helix:  0.06 (0.30), residues: 334
  sheet: -3.89 (0.23), residues: 352
  loop : -2.88 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 205 
 TYR   0.010   0.001   TYR D 240 
 PHE   0.020   0.002   PHE D 140 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.005   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10298)
  covalent geometry    : angle       0.70273 (13984)
  hydrogen bonds       : bond        0.03009 (  244)
  hydrogen bonds       : angle       4.30056 (  672)

********************** 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
  97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  211 GLN cc_start: 0.8492 (tp40) cc_final: 0.7628 (tm-30)
REVERT: A  304 MET cc_start: 0.7823 (ptm) cc_final: 0.7468 (ptm)
REVERT: B  283 MET cc_start: 0.8479 (mmt) cc_final: 0.7161 (mmt)
REVERT: B  389 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7577 (t0)
REVERT: B  476 TYR cc_start: 0.8350 (t80) cc_final: 0.8083 (t80)
REVERT: C   27 PHE cc_start: 0.6316 (t80) cc_final: 0.6039 (t80)
REVERT: D  420 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7546 (pp)
  outliers start: 13
  outliers final: 11
  residues processed: 92
  average time/residue: 0.0774
  time to fit residues: 11.2515
Evaluate side-chains
  93 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
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  389 ASP
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  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 54 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 125 optimal weight:    7.9990
   chunk 124 optimal weight:    0.8980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.146416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.129406 restraints weight = 15666.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.130629 restraints weight = 29123.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130899 restraints weight = 19633.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130550 restraints weight = 15669.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130763 restraints weight = 14432.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10298  Z= 0.151
  Angle     :  0.691  10.092  13984  Z= 0.340
  Chirality :  0.043   0.177   1570
  Planarity :  0.004   0.035   1828
  Dihedral  :  5.623  32.974   1444
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.20 %
    Favored  : 86.80 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.38 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.61 (0.23), residues: 1288
  helix:  0.08 (0.29), residues: 334
  sheet: -3.87 (0.23), residues: 352
  loop : -2.87 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 205 
 TYR   0.010   0.001   TYR B 240 
 PHE   0.029   0.002   PHE D 100 
 TRP   0.016   0.001   TRP C 328 
 HIS   0.005   0.001   HIS B 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10298)
  covalent geometry    : angle       0.69136 (13984)
  hydrogen bonds       : bond        0.02914 (  244)
  hydrogen bonds       : angle       4.27719 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1443.65 seconds
wall clock time: 25 minutes 48.12 seconds (1548.12 seconds total)