Starting phenix.real_space_refine
on Sat Aug 23 05:31:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ew2_28640/08_2025/8ew2_28640.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ew2_28640/08_2025/8ew2_28640.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ew2_28640/08_2025/8ew2_28640.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ew2_28640/08_2025/8ew2_28640.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ew2_28640/08_2025/8ew2_28640.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ew2_28640/08_2025/8ew2_28640.map"
  }
  resolution = 3.1
  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
-------------------------------------------------------------------------------
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=  -0.000 sd=   0.003
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      44      5.16       5
     C    6516      2.51       5
     N    1832      2.21       5
     O    1948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 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: 10340
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2585
          Classifications: {'peptide': 339}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320}
          Chain breaks: 1
  Time building chain proxies: 2.53, per 1000 atoms: 0.24
  Number of scatterers: 10340
  At special positions: 0
  Unit cell: (79.54, 97.58, 104.96, 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      44     16.00
     O    1948      8.00
     N    1832      7.00
     C    6516      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: 1.05
  Conformation dependent library (CDL) restraints added in 397.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2488

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 8 sheets defined
      54.1% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 35 through 47
    Processing helix  chain 'B' and resid 51 through 64
    Processing helix  chain 'B' and resid 79 through 85
      removed outlier: 3.968A  pdb=" N   TYR B  84 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 129 through 140
    Processing helix  chain 'B' and resid 159 through 180
    Processing helix  chain 'B' and resid 197 through 219
    Processing helix  chain 'B' and resid 222 through 226
    Processing helix  chain 'B' and resid 244 through 260
      removed outlier: 3.536A  pdb=" N   THR B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 288
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 6.790A  pdb=" N   SER B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   ALA B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 339
    Processing helix  chain 'A' and resid 8 through 23
    Processing helix  chain 'A' and resid 35 through 45
    Processing helix  chain 'A' and resid 51 through 64
      removed outlier: 3.585A  pdb=" N   ARG A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 85
      removed outlier: 3.984A  pdb=" N   TYR A  84 " --> pdb=" O   HIS A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 129 through 140
    Processing helix  chain 'A' and resid 159 through 180
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 222 through 226
    Processing helix  chain 'A' and resid 244 through 260
      removed outlier: 3.540A  pdb=" N   THR A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 288
    Processing helix  chain 'A' and resid 302 through 312
      removed outlier: 6.840A  pdb=" N   SER A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   ALA A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 339
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 35 through 46
    Processing helix  chain 'C' and resid 51 through 64
    Processing helix  chain 'C' and resid 66 through 70
    Processing helix  chain 'C' and resid 79 through 85
    Processing helix  chain 'C' and resid 92 through 98
    Processing helix  chain 'C' and resid 129 through 140
    Processing helix  chain 'C' and resid 159 through 180
    Processing helix  chain 'C' and resid 197 through 219
    Processing helix  chain 'C' and resid 222 through 226
    Processing helix  chain 'C' and resid 244 through 260
      removed outlier: 3.552A  pdb=" N   THR C 259 " --> pdb=" O   ALA C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 275 through 288
    Processing helix  chain 'C' and resid 302 through 314
      removed outlier: 6.514A  pdb=" N   SER C 308 " --> pdb=" O   ALA C 304 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ALA C 309 " --> pdb=" O   LEU C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 339
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 35 through 46
      removed outlier: 3.756A  pdb=" N   ILE D  46 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 79 through 85
      removed outlier: 3.968A  pdb=" N   TYR D  84 " --> pdb=" O   HIS D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 92 through 100
    Processing helix  chain 'D' and resid 129 through 140
    Processing helix  chain 'D' and resid 159 through 180
    Processing helix  chain 'D' and resid 197 through 219
    Processing helix  chain 'D' and resid 222 through 226
    Processing helix  chain 'D' and resid 244 through 260
      removed outlier: 3.525A  pdb=" N   THR D 259 " --> pdb=" O   ALA D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 275 through 288
    Processing helix  chain 'D' and resid 302 through 314
      removed outlier: 6.314A  pdb=" N   SER D 308 " --> pdb=" O   ALA D 304 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   ALA D 309 " --> pdb=" O   LEU D 305 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 321 through 340
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 31
      removed outlier: 6.586A  pdb=" N   GLY B  28 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   VAL B  76 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 5.778A  pdb=" N   LEU B  78 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 5.852A  pdb=" N   ALA B 145 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   ILE B 106 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASP B 143 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ILE B 185 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ALA B 145 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLU B 187 " --> pdb=" O   ALA B 145 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   TRP B 147 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLU B 189 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   CYS B 149 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU B 191 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU B 151 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 114
    Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31
      removed outlier: 6.805A  pdb=" N   GLY A  28 " --> pdb=" O   GLY A  74 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   VAL A  76 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A  30 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 5.693A  pdb=" N   LEU A  78 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   VAL A 104 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   ALA A 145 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 5.465A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASP A 143 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   ILE A 185 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ALA A 145 " --> pdb=" O   ILE A 185 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   GLU A 187 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TRP A 147 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   GLU A 189 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   CYS A 149 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU A 191 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LEU A 151 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   LEU A 228 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114
    Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31
      removed outlier: 6.959A  pdb=" N   GLY C  28 " --> pdb=" O   GLY C  74 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL C  76 " --> pdb=" O   GLY C  28 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   LEU C  30 " --> pdb=" O   VAL C  76 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA C 145 " --> pdb=" O   ILE C 185 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   GLU C 187 " --> pdb=" O   ALA C 145 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   TRP C 147 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   GLU C 189 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   CYS C 149 " --> pdb=" O   GLU C 189 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LEU C 191 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   LEU C 151 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LEU C 228 " --> pdb=" O   THR C 268 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   VAL C 267 " --> pdb=" O   THR C 298 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   SER C 300 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   PHE C 269 " --> pdb=" O   SER C 300 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114
    Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31
      removed outlier: 6.310A  pdb=" N   GLY D  28 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   ILE D  77 " --> pdb=" O   GLY D  28 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU D  30 " --> pdb=" O   ILE D  77 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU D 228 " --> pdb=" O   THR D 268 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   VAL D 267 " --> pdb=" O   THR D 298 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   SER D 300 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   PHE D 269 " --> pdb=" O   SER D 300 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114

    571 hydrogen bonds defined for protein.
    1656 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: 1.79

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3441
        1.34 -     1.46: 1498
        1.46 -     1.57: 5536
        1.57 -     1.69: 1
        1.69 -     1.81: 56
  Bond restraints: 10532
  Sorted by residual:
  bond pdb=" CB  PRO D  71 "
       pdb=" CG  PRO D  71 "
    ideal  model  delta    sigma   weight residual
    1.492  1.600 -0.108 5.00e-02 4.00e+02 4.67e+00
  bond pdb=" C   ASN C  70 "
       pdb=" N   PRO C  71 "
    ideal  model  delta    sigma   weight residual
    1.331  1.348 -0.017 7.90e-03 1.60e+04 4.55e+00
  bond pdb=" C   ASN A  70 "
       pdb=" N   PRO A  71 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.015 9.40e-03 1.13e+04 2.40e+00
  bond pdb=" CG1 ILE D  77 "
       pdb=" CD1 ILE D  77 "
    ideal  model  delta    sigma   weight residual
    1.513  1.458  0.055 3.90e-02 6.57e+02 2.00e+00
  bond pdb=" CB  GLN C  95 "
       pdb=" CG  GLN C  95 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.64e+00
  ... (remaining 10527 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 14040
        2.12 -     4.25: 199
        4.25 -     6.37: 25
        6.37 -     8.50: 3
        8.50 -    10.62: 1
  Bond angle restraints: 14268
  Sorted by residual:
  angle pdb=" CA  PRO D  71 "
        pdb=" N   PRO D  71 "
        pdb=" CD  PRO D  71 "
      ideal   model   delta    sigma   weight residual
     112.00  105.58    6.42 1.40e+00 5.10e-01 2.10e+01
  angle pdb=" N   VAL B  23 "
        pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     106.21  110.54   -4.33 1.07e+00 8.73e-01 1.63e+01
  angle pdb=" C   THR A  51 "
        pdb=" N   GLU A  52 "
        pdb=" CA  GLU A  52 "
      ideal   model   delta    sigma   weight residual
     120.82  125.63   -4.81 1.50e+00 4.44e-01 1.03e+01
  angle pdb=" N   GLU A  49 "
        pdb=" CA  GLU A  49 "
        pdb=" C   GLU A  49 "
      ideal   model   delta    sigma   weight residual
     107.73  111.89   -4.16 1.34e+00 5.57e-01 9.63e+00
  angle pdb=" N   THR A  51 "
        pdb=" CA  THR A  51 "
        pdb=" C   THR A  51 "
      ideal   model   delta    sigma   weight residual
     110.35  114.64   -4.29 1.40e+00 5.10e-01 9.39e+00
  ... (remaining 14263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5508
       17.98 -    35.97: 694
       35.97 -    53.95: 167
       53.95 -    71.94: 39
       71.94 -    89.92: 12
  Dihedral angle restraints: 6420
    sinusoidal: 2540
      harmonic: 3880
  Sorted by residual:
  dihedral pdb=" CA  ALA A 304 "
           pdb=" C   ALA A 304 "
           pdb=" N   LEU A 305 "
           pdb=" CA  LEU A 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.78   18.22     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CB  GLU B 132 "
           pdb=" CG  GLU B 132 "
           pdb=" CD  GLU B 132 "
           pdb=" OE1 GLU B 132 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.92   89.92     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CA  ASP C  88 "
           pdb=" CB  ASP C  88 "
           pdb=" CG  ASP C  88 "
           pdb=" OD1 ASP C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.17   56.17     1      2.00e+01 2.50e-03 1.06e+01
  ... (remaining 6417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 936
       0.026 -    0.051: 393
       0.051 -    0.077: 158
       0.077 -    0.102: 99
       0.102 -    0.128: 42
  Chirality restraints: 1628
  Sorted by residual:
  chirality pdb=" CA  ILE B 190 "
            pdb=" N   ILE B 190 "
            pdb=" C   ILE B 190 "
            pdb=" CB  ILE B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE D 182 "
            pdb=" N   ILE D 182 "
            pdb=" C   ILE D 182 "
            pdb=" CB  ILE D 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  TYR C  84 "
            pdb=" N   TYR C  84 "
            pdb=" C   TYR C  84 "
            pdb=" CB  TYR C  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 1625 not shown)

  Planarity restraints: 1848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  70 "    0.044 5.00e-02 4.00e+02   6.38e-02 6.52e+00
        pdb=" N   PRO D  71 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO D  71 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO D  71 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 187 "   -0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO A 188 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 188 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 188 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A   8 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.61e+00
        pdb=" N   PRO A   9 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO A   9 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A   9 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1845 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 662
        2.73 -     3.27: 10885
        3.27 -     3.82: 19395
        3.82 -     4.36: 23068
        4.36 -     4.90: 38736
  Nonbonded interactions: 92746
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 121 "
            pdb=" OG  SER A 159 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" NZ  LYS B 146 "
            pdb=" OE1 GLU B 187 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OE1 GLU A  81 "
            pdb=" NE2 GLN A  85 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" NZ  LYS C 207 "
            pdb=" O   SER D 217 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   GLN B  60 "
            pdb=" OG1 THR B  64 "
     model   vdw
     2.230 3.040
  ... (remaining 92741 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  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:                    0.030
  Process input model:                     11.000
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
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      :  0.004   0.108  10532  Z= 0.160
  Angle     :  0.626  10.619  14268  Z= 0.353
  Chirality :  0.040   0.128   1628
  Planarity :  0.005   0.064   1848
  Dihedral  : 17.049  89.921   3932
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 21.72 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.64 (0.24), residues: 1340
  helix:  1.69 (0.19), residues: 696
  sheet: -1.46 (0.38), residues: 192
  loop : -0.61 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  42 
 TYR   0.026   0.002   TYR B  58 
 PHE   0.010   0.001   PHE A  93 
 TRP   0.006   0.001   TRP A 147 
 HIS   0.003   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 (10532)
  covalent geometry    : angle       0.62630 (14268)
  hydrogen bonds       : bond        0.11285 (  571)
  hydrogen bonds       : angle       5.26921 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.431 
Fit side-chains
REVERT: C   84 TYR cc_start: 0.6279 (m-10) cc_final: 0.6030 (m-10)
  outliers start: 5
  outliers final: 4
  residues processed: 118
  average time/residue: 0.1070
  time to fit residues: 18.1460
Evaluate side-chains
  109 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  325 GLU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   77 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0370
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    2.6066

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
B 324 GLN
A  11 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  11 GLN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.141534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.109494 restraints weight = 14123.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.88
r_work: 0.3166 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.0856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.090  10532  Z= 0.247
  Angle     :  0.608   6.914  14268  Z= 0.314
  Chirality :  0.043   0.139   1628
  Planarity :  0.005   0.056   1848
  Dihedral  :  5.026  59.626   1460
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 17.79 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.41 (0.23), residues: 1340
  helix:  1.54 (0.19), residues: 696
  sheet: -1.32 (0.35), residues: 216
  loop : -0.87 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 258 
 TYR   0.026   0.002   TYR D 213 
 PHE   0.012   0.002   PHE A  93 
 TRP   0.015   0.002   TRP D 147 
 HIS   0.003   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 (10532)
  covalent geometry    : angle       0.60840 (14268)
  hydrogen bonds       : bond        0.03906 (  571)
  hydrogen bonds       : angle       4.65382 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 114
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B  270 LEU cc_start: 0.8293 (tt) cc_final: 0.8080 (tt)
REVERT: C   84 TYR cc_start: 0.6861 (m-10) cc_final: 0.6640 (m-10)
REVERT: C  303 ARG cc_start: 0.8188 (ptt180) cc_final: 0.7235 (ttt180)
REVERT: D  173 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8922 (t80)
REVERT: D  295 TRP cc_start: 0.9143 (OUTLIER) cc_final: 0.7205 (m-90)
  outliers start: 46
  outliers final: 33
  residues processed: 142
  average time/residue: 0.1289
  time to fit residues: 24.9184
Evaluate side-chains
  139 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   95 GLN
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  139 LYS
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   83 LEU
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  328 VAL
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   66 ASP
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  329 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 60 optimal weight:    7.9990
   chunk 124 optimal weight:    0.0170
   chunk 23 optimal weight:    6.9990
   chunk 110 optimal weight:    0.0010
   chunk 131 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 130 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.9826

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  50 ASN
C  85 GLN
C 166 ASN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.146343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.116085 restraints weight = 14028.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.83
r_work: 0.3254 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.0987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10532  Z= 0.139
  Angle     :  0.512   6.529  14268  Z= 0.264
  Chirality :  0.040   0.127   1628
  Planarity :  0.004   0.044   1848
  Dihedral  :  4.402  35.761   1455
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 18.98 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.66 (0.24), residues: 1340
  helix:  1.84 (0.19), residues: 696
  sheet: -1.42 (0.34), residues: 216
  loop : -0.83 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 148 
 TYR   0.016   0.002   TYR D 213 
 PHE   0.010   0.001   PHE C 144 
 TRP   0.008   0.001   TRP D 147 
 HIS   0.004   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10532)
  covalent geometry    : angle       0.51228 (14268)
  hydrogen bonds       : bond        0.03330 (  571)
  hydrogen bonds       : angle       4.37405 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 128
  time to evaluate  : 0.429 
Fit side-chains
REVERT: B  295 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.8493 (m-90)
REVERT: B  330 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8223 (mmp-170)
REVERT: A  106 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8768 (tt)
REVERT: A  189 GLU cc_start: 0.7882 (tt0) cc_final: 0.7626 (tp30)
REVERT: C  303 ARG cc_start: 0.8245 (ptt180) cc_final: 0.7288 (ttt180)
REVERT: D   36 THR cc_start: 0.7125 (m) cc_final: 0.6785 (t)
REVERT: D  173 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8843 (t80)
  outliers start: 47
  outliers final: 27
  residues processed: 156
  average time/residue: 0.1257
  time to fit residues: 26.5687
Evaluate side-chains
  146 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0270
   chunk 70 optimal weight:    6.9990
   chunk 119 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0050
   chunk 73 optimal weight:   10.0000
   chunk 105 optimal weight:    5.9990
   overall best weight:    1.1856

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.144984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.113182 restraints weight = 14159.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.91
r_work: 0.3217 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8642
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10532  Z= 0.147
  Angle     :  0.519   6.396  14268  Z= 0.264
  Chirality :  0.040   0.140   1628
  Planarity :  0.004   0.042   1848
  Dihedral  :  4.265  35.633   1455
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 19.34 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.74 (0.24), residues: 1340
  helix:  1.96 (0.19), residues: 696
  sheet: -1.45 (0.34), residues: 216
  loop : -0.86 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 303 
 TYR   0.018   0.002   TYR D 213 
 PHE   0.010   0.001   PHE C 144 
 TRP   0.009   0.002   TRP A 147 
 HIS   0.003   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (10532)
  covalent geometry    : angle       0.51932 (14268)
  hydrogen bonds       : bond        0.03222 (  571)
  hydrogen bonds       : angle       4.24917 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 122
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
REVERT: B  173 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8986 (t80)
REVERT: B  293 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8751 (mtmm)
REVERT: B  295 TRP cc_start: 0.9018 (OUTLIER) cc_final: 0.8587 (m-90)
REVERT: B  330 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8371 (mmp-170)
REVERT: A   84 TYR cc_start: 0.7884 (m-80) cc_final: 0.7606 (m-10)
REVERT: A  106 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8761 (tt)
REVERT: A  295 TRP cc_start: 0.9059 (OUTLIER) cc_final: 0.7270 (m-90)
REVERT: A  329 LYS cc_start: 0.8209 (pptt) cc_final: 0.7971 (ptmt)
REVERT: C  303 ARG cc_start: 0.8144 (ptt180) cc_final: 0.7290 (ttt180)
REVERT: D   36 THR cc_start: 0.6967 (m) cc_final: 0.6678 (t)
REVERT: D  173 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8800 (t80)
  outliers start: 53
  outliers final: 34
  residues processed: 155
  average time/residue: 0.1307
  time to fit residues: 27.6300
Evaluate side-chains
  155 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 114
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  173 TYR
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  295 TRP
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain B residue  338 CYS
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 101 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 110 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 100 optimal weight:    0.8980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 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 = 0.3739 r_free = 0.3739 target = 0.141783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.109803 restraints weight = 14224.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.90
r_work: 0.3166 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.1442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078  10532  Z= 0.211
  Angle     :  0.569   6.193  14268  Z= 0.290
  Chirality :  0.042   0.135   1628
  Planarity :  0.004   0.045   1848
  Dihedral  :  4.410  38.392   1455
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 18.89 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.57 (0.23), residues: 1340
  helix:  1.78 (0.19), residues: 696
  sheet: -1.31 (0.36), residues: 196
  loop : -1.04 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 148 
 TYR   0.024   0.002   TYR D 213 
 PHE   0.011   0.002   PHE C 144 
 TRP   0.015   0.002   TRP D 147 
 HIS   0.003   0.001   HIS C  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (10532)
  covalent geometry    : angle       0.56853 (14268)
  hydrogen bonds       : bond        0.03531 (  571)
  hydrogen bonds       : angle       4.30522 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 119
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A  106 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8752 (tt)
REVERT: A  173 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.9039 (t80)
REVERT: A  329 LYS cc_start: 0.8240 (pptt) cc_final: 0.8019 (ptmt)
REVERT: C  295 TRP cc_start: 0.9072 (OUTLIER) cc_final: 0.7615 (m-90)
REVERT: C  303 ARG cc_start: 0.8207 (ptt180) cc_final: 0.7314 (ttt180)
REVERT: D   36 THR cc_start: 0.7037 (m) cc_final: 0.6726 (t)
REVERT: D  295 TRP cc_start: 0.9099 (OUTLIER) cc_final: 0.7166 (m-90)
  outliers start: 57
  outliers final: 40
  residues processed: 154
  average time/residue: 0.1282
  time to fit residues: 27.0522
Evaluate side-chains
  158 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 114
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  139 LYS
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  321 LYS
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  338 CYS
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  173 TYR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 106 optimal weight:    7.9990
   chunk 130 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
A 231 ASN
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.142786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.110969 restraints weight = 14258.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 1.91
r_work: 0.3185 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10532  Z= 0.171
  Angle     :  0.541   6.441  14268  Z= 0.275
  Chirality :  0.041   0.130   1628
  Planarity :  0.004   0.046   1848
  Dihedral  :  4.332  36.678   1455
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 19.62 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.63 (0.23), residues: 1340
  helix:  1.85 (0.19), residues: 696
  sheet: -1.45 (0.34), residues: 216
  loop : -0.90 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 330 
 TYR   0.020   0.002   TYR A 213 
 PHE   0.010   0.001   PHE C 144 
 TRP   0.011   0.002   TRP A 147 
 HIS   0.004   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (10532)
  covalent geometry    : angle       0.54136 (14268)
  hydrogen bonds       : bond        0.03341 (  571)
  hydrogen bonds       : angle       4.23975 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 119
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A  106 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8740 (tt)
REVERT: A  295 TRP cc_start: 0.9050 (OUTLIER) cc_final: 0.7365 (m-90)
REVERT: A  332 LEU cc_start: 0.8643 (tt) cc_final: 0.8098 (mt)
REVERT: C   84 TYR cc_start: 0.6963 (m-10) cc_final: 0.6510 (m-10)
REVERT: C  295 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.7526 (m-90)
REVERT: C  303 ARG cc_start: 0.8163 (ptt180) cc_final: 0.7281 (ttt180)
REVERT: D   36 THR cc_start: 0.7022 (m) cc_final: 0.6755 (t)
REVERT: D  295 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.7126 (m-90)
  outliers start: 54
  outliers final: 34
  residues processed: 155
  average time/residue: 0.1270
  time to fit residues: 27.1135
Evaluate side-chains
  153 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  232 MET
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  335 SER
Chi-restraints excluded: chain B residue  338 CYS
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  295 TRP
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0980
   chunk 64 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 105 optimal weight:    0.2980
   chunk 89 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 123 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 121 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 274 GLN
A 334 ASN
D 231 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.145475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.114347 restraints weight = 14115.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.90
r_work: 0.3239 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3096 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10532  Z= 0.118
  Angle     :  0.507   6.566  14268  Z= 0.259
  Chirality :  0.039   0.128   1628
  Planarity :  0.004   0.043   1848
  Dihedral  :  4.134  34.041   1455
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.89 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.77 (0.23), residues: 1340
  helix:  2.07 (0.19), residues: 696
  sheet: -1.80 (0.36), residues: 176
  loop : -0.91 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.016   0.001   TYR C  84 
 PHE   0.010   0.001   PHE C 144 
 TRP   0.008   0.001   TRP C 295 
 HIS   0.004   0.000   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10532)
  covalent geometry    : angle       0.50745 (14268)
  hydrogen bonds       : bond        0.03016 (  571)
  hydrogen bonds       : angle       4.10338 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 130
  time to evaluate  : 0.435 
Fit side-chains
REVERT: B  293 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8705 (mtmm)
REVERT: A   83 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8515 (tp)
REVERT: A  106 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8776 (tt)
REVERT: A  332 LEU cc_start: 0.8614 (tt) cc_final: 0.7960 (mt)
REVERT: C   84 TYR cc_start: 0.6900 (m-10) cc_final: 0.6634 (m-10)
REVERT: C  303 ARG cc_start: 0.8133 (ptt180) cc_final: 0.7302 (ttt180)
REVERT: D  173 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8826 (t80)
REVERT: D  199 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8305 (mmmt)
REVERT: D  295 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.7294 (m-90)
  outliers start: 41
  outliers final: 27
  residues processed: 158
  average time/residue: 0.1305
  time to fit residues: 27.9628
Evaluate side-chains
  154 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 122
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  338 CYS
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 86 optimal weight:    3.9990
   chunk 102 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.146502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116675 restraints weight = 14154.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.87
r_work: 0.3229 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10532  Z= 0.130
  Angle     :  0.517   6.370  14268  Z= 0.262
  Chirality :  0.039   0.143   1628
  Planarity :  0.004   0.050   1848
  Dihedral  :  3.980  20.688   1454
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 21.62 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.81 (0.23), residues: 1340
  helix:  2.11 (0.19), residues: 696
  sheet: -1.78 (0.36), residues: 176
  loop : -0.91 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  68 
 TYR   0.018   0.001   TYR D 213 
 PHE   0.010   0.001   PHE D 144 
 TRP   0.008   0.001   TRP D 295 
 HIS   0.004   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10532)
  covalent geometry    : angle       0.51655 (14268)
  hydrogen bonds       : bond        0.03005 (  571)
  hydrogen bonds       : angle       4.05621 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.394 
Fit side-chains
REVERT: B  293 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8719 (mtmm)
REVERT: A  106 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8769 (tt)
REVERT: A  295 TRP cc_start: 0.8985 (OUTLIER) cc_final: 0.7400 (m-90)
REVERT: A  303 ARG cc_start: 0.7273 (ptm160) cc_final: 0.6943 (ttt180)
REVERT: A  332 LEU cc_start: 0.8507 (tt) cc_final: 0.7981 (mt)
REVERT: C   84 TYR cc_start: 0.6810 (m-10) cc_final: 0.6582 (m-10)
REVERT: C  303 ARG cc_start: 0.8180 (ptt180) cc_final: 0.7364 (ttt180)
REVERT: D  173 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (t80)
REVERT: D  199 LYS cc_start: 0.8564 (ttpp) cc_final: 0.8284 (mmmt)
REVERT: D  295 TRP cc_start: 0.9009 (OUTLIER) cc_final: 0.7329 (m-90)
  outliers start: 39
  outliers final: 30
  residues processed: 150
  average time/residue: 0.1191
  time to fit residues: 24.3864
Evaluate side-chains
  151 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 116
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Chi-restraints excluded: chain D residue  338 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 116 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 60 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN
** D 231 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 = 0.3755 r_free = 0.3755 target = 0.143108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.111470 restraints weight = 14210.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 1.90
r_work: 0.3198 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10532  Z= 0.169
  Angle     :  0.540   5.965  14268  Z= 0.274
  Chirality :  0.041   0.150   1628
  Planarity :  0.004   0.048   1848
  Dihedral  :  4.046  22.664   1454
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 20.99 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.78 (0.23), residues: 1340
  helix:  2.02 (0.19), residues: 696
  sheet: -1.49 (0.34), residues: 216
  loop : -0.85 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 330 
 TYR   0.026   0.002   TYR B 213 
 PHE   0.010   0.001   PHE D 144 
 TRP   0.011   0.002   TRP D 147 
 HIS   0.002   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10532)
  covalent geometry    : angle       0.53964 (14268)
  hydrogen bonds       : bond        0.03207 (  571)
  hydrogen bonds       : angle       4.10410 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 0.423 
Fit side-chains
REVERT: B  293 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8739 (mtmm)
REVERT: A  106 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8790 (tt)
REVERT: A  295 TRP cc_start: 0.9026 (OUTLIER) cc_final: 0.7423 (m-90)
REVERT: A  303 ARG cc_start: 0.7285 (ptm160) cc_final: 0.6984 (ttt180)
REVERT: A  332 LEU cc_start: 0.8534 (tt) cc_final: 0.8024 (mt)
REVERT: C   84 TYR cc_start: 0.6952 (m-10) cc_final: 0.6674 (m-10)
REVERT: C  303 ARG cc_start: 0.8171 (ptt180) cc_final: 0.7351 (ttt180)
REVERT: D  173 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8821 (t80)
REVERT: D  295 TRP cc_start: 0.9045 (OUTLIER) cc_final: 0.7327 (m-90)
  outliers start: 40
  outliers final: 31
  residues processed: 142
  average time/residue: 0.1096
  time to fit residues: 21.4677
Evaluate side-chains
  151 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  274 GLN
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   chunk 97 optimal weight:    8.9990
   chunk 89 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0370
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 274 GLN
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.145381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.115730 restraints weight = 14125.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.81
r_work: 0.3246 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10532  Z= 0.121
  Angle     :  0.514   5.963  14268  Z= 0.261
  Chirality :  0.039   0.145   1628
  Planarity :  0.004   0.046   1848
  Dihedral  :  3.962  20.225   1454
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 21.26 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.86 (0.24), residues: 1340
  helix:  2.15 (0.19), residues: 696
  sheet: -1.80 (0.36), residues: 176
  loop : -0.88 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 303 
 TYR   0.015   0.001   TYR C  84 
 PHE   0.010   0.001   PHE D 144 
 TRP   0.008   0.001   TRP D 295 
 HIS   0.004   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (10532)
  covalent geometry    : angle       0.51384 (14268)
  hydrogen bonds       : bond        0.02958 (  571)
  hydrogen bonds       : angle       4.03158 ( 1656)

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

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

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2680 Ramachandran restraints generated.
    1340 Oldfield, 0 Emsley, 1340 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: B  293 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8727 (mtmm)
REVERT: A  106 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8770 (tt)
REVERT: A  295 TRP cc_start: 0.8952 (OUTLIER) cc_final: 0.7501 (m-90)
REVERT: A  303 ARG cc_start: 0.7303 (ptm160) cc_final: 0.7020 (ttt180)
REVERT: A  332 LEU cc_start: 0.8550 (tt) cc_final: 0.8066 (mt)
REVERT: C   80 HIS cc_start: 0.7466 (t-170) cc_final: 0.6958 (t-170)
REVERT: C   84 TYR cc_start: 0.6731 (m-10) cc_final: 0.6408 (m-10)
REVERT: C  303 ARG cc_start: 0.8193 (ptt180) cc_final: 0.7420 (ttt180)
REVERT: D  173 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8777 (t80)
REVERT: D  199 LYS cc_start: 0.8541 (ttpp) cc_final: 0.8296 (mmmt)
REVERT: D  295 TRP cc_start: 0.8972 (OUTLIER) cc_final: 0.7514 (m-90)
  outliers start: 39
  outliers final: 29
  residues processed: 142
  average time/residue: 0.1168
  time to fit residues: 22.9103
Evaluate side-chains
  147 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  164 MET
Chi-restraints excluded: chain B residue  182 ILE
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  293 LYS
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  343 THR
Chi-restraints excluded: chain A residue    4 HIS
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  295 TRP
Chi-restraints excluded: chain C residue   35 SER
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  164 MET
Chi-restraints excluded: chain C residue  332 LEU
Chi-restraints excluded: chain C residue  338 CYS
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  173 TYR
Chi-restraints excluded: chain D residue  259 THR
Chi-restraints excluded: chain D residue  278 GLU
Chi-restraints excluded: chain D residue  295 TRP
Chi-restraints excluded: chain D residue  321 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 112 optimal weight:    7.9990
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 274 GLN
** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.143812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.112077 restraints weight = 14169.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.90
r_work: 0.3208 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10532  Z= 0.169
  Angle     :  0.557   7.172  14268  Z= 0.284
  Chirality :  0.040   0.149   1628
  Planarity :  0.004   0.046   1848
  Dihedral  :  4.010  22.214   1454
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 21.17 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.75 (0.23), residues: 1340
  helix:  2.05 (0.19), residues: 696
  sheet: -1.77 (0.37), residues: 176
  loop : -0.94 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 258 
 TYR   0.020   0.002   TYR B 213 
 PHE   0.010   0.001   PHE D 144 
 TRP   0.011   0.002   TRP D 147 
 HIS   0.003   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10532)
  covalent geometry    : angle       0.55696 (14268)
  hydrogen bonds       : bond        0.03167 (  571)
  hydrogen bonds       : angle       4.07093 ( 1656)

===============================================================================
Job complete
usr+sys time: 2714.46 seconds
wall clock time: 47 minutes 30.88 seconds (2850.88 seconds total)