Starting phenix.real_space_refine
on Tue Mar  3 17:43:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nnu_12484/03_2026/7nnu_12484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nnu_12484/03_2026/7nnu_12484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2026/7nnu_12484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2026/7nnu_12484.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2026/7nnu_12484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nnu_12484/03_2026/7nnu_12484.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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      36      5.16       5
     C    5004      2.51       5
     N    1266      2.21       5
     O    1418      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7724
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2137
          Classifications: {'peptide': 279}
          Link IDs: {'PTRANS': 13, 'TRANS': 265}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2131
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 12, 'TRANS': 260}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1321
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 4, 'TRANS': 164}
    Chain: "D"
      Number of atoms: 2100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2100
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 9, 'TRANS': 251}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
  Time building chain proxies: 1.82, per 1000 atoms: 0.24
  Number of scatterers: 7724
  At special positions: 0
  Unit cell: (87.894, 105.627, 100.23, 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      36     16.00
     O    1418      8.00
     N    1266      7.00
     C    5004      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: 0.72
  Conformation dependent library (CDL) restraints added in 289.1 milliseconds
  

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 5 sheets defined
      63.7% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 47
      No H-bonds generated for 'chain 'A' and resid 45 through 47'
    Processing helix  chain 'A' and resid 48 through 54
    Processing helix  chain 'A' and resid 78 through 84
    Processing helix  chain 'A' and resid 101 through 107
    Processing helix  chain 'A' and resid 107 through 113
    Processing helix  chain 'A' and resid 116 through 131
    Processing helix  chain 'A' and resid 133 through 137
      removed outlier: 4.022A  pdb=" N   ALA A 137 " --> pdb=" O   ALA A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 145 through 160
      removed outlier: 4.188A  pdb=" N   VAL A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 194
      removed outlier: 3.578A  pdb=" N   GLN A 181 " --> pdb=" O   GLU A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 209
      removed outlier: 3.772A  pdb=" N   GLY A 209 " --> pdb=" O   GLU A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 4.098A  pdb=" N   LEU A 237 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 257
    Processing helix  chain 'A' and resid 267 through 281
      removed outlier: 3.578A  pdb=" N   LEU A 278 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 54
      removed outlier: 4.119A  pdb=" N   ASN B  54 " --> pdb=" O   MET B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 86
      removed outlier: 3.541A  pdb=" N   LEU B  83 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS B  86 " --> pdb=" O   ASP B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 98
      removed outlier: 3.538A  pdb=" N   LEU B  98 " --> pdb=" O   GLU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 4.562A  pdb=" N   GLY B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 117 through 132
    Processing helix  chain 'B' and resid 142 through 146
      removed outlier: 3.694A  pdb=" N   LEU B 146 " --> pdb=" O   PRO B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 161
    Processing helix  chain 'B' and resid 177 through 194
    Processing helix  chain 'B' and resid 205 through 212
    Processing helix  chain 'B' and resid 228 through 233
    Processing helix  chain 'B' and resid 235 through 242
      removed outlier: 3.737A  pdb=" N   LEU B 239 " --> pdb=" O   ASP B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 260
    Processing helix  chain 'B' and resid 269 through 281
    Processing helix  chain 'C' and resid 12 through 31
    Processing helix  chain 'C' and resid 43 through 76
      removed outlier: 3.930A  pdb=" N   GLY C  47 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      Proline residue:  C  57  - end of helix
    Processing helix  chain 'C' and resid 82 through 101
      removed outlier: 3.769A  pdb=" N   THR C  86 " --> pdb=" O   PHE C  82 " (cutoff:3.500A)
      Proline residue:  C  93  - end of helix
    Processing helix  chain 'C' and resid 106 through 121
    Processing helix  chain 'C' and resid 124 through 134
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 147 through 150
      removed outlier: 3.652A  pdb=" N   MET C 150 " --> pdb=" O   LEU C 147 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 147 through 150'
    Processing helix  chain 'C' and resid 151 through 172
      removed outlier: 3.869A  pdb=" N   ILE C 155 " --> pdb=" O   ILE C 151 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLU C 165 " --> pdb=" O   TRP C 161 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL C 170 " --> pdb=" O   GLY C 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 19
      removed outlier: 3.705A  pdb=" N   ARG D  18 " --> pdb=" O   THR D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 37
      removed outlier: 3.581A  pdb=" N   LEU D  37 " --> pdb=" O   ILE D  33 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 59
      removed outlier: 3.731A  pdb=" N   GLY D  59 " --> pdb=" O   VAL D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 70
      removed outlier: 4.036A  pdb=" N   PHE D  65 " --> pdb=" O   LYS D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 87
    Processing helix  chain 'D' and resid 102 through 129
    Processing helix  chain 'D' and resid 131 through 143
    Processing helix  chain 'D' and resid 144 through 150
    Processing helix  chain 'D' and resid 152 through 184
      Proline residue:  D 168  - end of helix
      removed outlier: 3.714A  pdb=" N   ARG D 184 " --> pdb=" O   ALA D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 192 through 199
    Processing helix  chain 'D' and resid 200 through 225
      Proline residue:  D 206  - end of helix
    Processing helix  chain 'D' and resid 242 through 244
      No H-bonds generated for 'chain 'D' and resid 242 through 244'
    Processing helix  chain 'D' and resid 245 through 263
      removed outlier: 3.843A  pdb=" N   VAL D 249 " --> pdb=" O   ASP D 245 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 31
      removed outlier: 6.791A  pdb=" N   SER A  24 " --> pdb=" O   HIS A  10 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   HIS A  10 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   LEU A  26 " --> pdb=" O   PHE A   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89
      removed outlier: 6.581A  pdb=" N   TRP A  35 " --> pdb=" O   GLN A 212 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   LEU A 214 " --> pdb=" O   TRP A  35 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ALA A  37 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE A  39 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL A 213 " --> pdb=" O   GLN A 224 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   GLN A 224 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL A 215 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 30
      removed outlier: 6.198A  pdb=" N   ASP B  24 " --> pdb=" O   SER B   9 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   SER B   9 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   LEU B  26 " --> pdb=" O   ASN B   7 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   PHE B  28 " --> pdb=" O   PHE B   5 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL B   8 " --> pdb=" O   SER B  61 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER B  61 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90
      removed outlier: 6.364A  pdb=" N   ILE B 167 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   VAL B 201 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   LEU B 169 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE B  36 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   PHE B  35 " --> pdb=" O   ASP B 214 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   LEU B 216 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ALA B  37 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 7.487A  pdb=" N   LEU B 218 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL B  39 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   GLU B 219 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 5.684A  pdb=" N   LEU B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 34

    445 hydrogen bonds defined for protein.
    1287 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: 1.23

  Time building geometry restraints manager: 0.93 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: 2334
        1.34 -     1.46: 1497
        1.46 -     1.58: 3951
        1.58 -     1.70: 0
        1.70 -     1.82: 68
  Bond restraints: 7850
  Sorted by residual:
  bond pdb=" CG1 ILE C  74 "
       pdb=" CD1 ILE C  74 "
    ideal  model  delta    sigma   weight residual
    1.513  1.390  0.123 3.90e-02 6.57e+02 9.95e+00
  bond pdb=" CG  LEU D 164 "
       pdb=" CD1 LEU D 164 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.88e+00
  bond pdb=" CG  LEU A  74 "
       pdb=" CD1 LEU A  74 "
    ideal  model  delta    sigma   weight residual
    1.521  1.466  0.055 3.30e-02 9.18e+02 2.77e+00
  bond pdb=" CB  PRO D 202 "
       pdb=" CG  PRO D 202 "
    ideal  model  delta    sigma   weight residual
    1.492  1.411  0.081 5.00e-02 4.00e+02 2.61e+00
  bond pdb=" CG  PRO D 206 "
       pdb=" CD  PRO D 206 "
    ideal  model  delta    sigma   weight residual
    1.503  1.449  0.054 3.40e-02 8.65e+02 2.57e+00
  ... (remaining 7845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 10080
        1.53 -     3.06: 425
        3.06 -     4.60: 90
        4.60 -     6.13: 21
        6.13 -     7.66: 14
  Bond angle restraints: 10630
  Sorted by residual:
  angle pdb=" C   PHE A  13 "
        pdb=" N   THR A  14 "
        pdb=" CA  THR A  14 "
      ideal   model   delta    sigma   weight residual
     121.70  128.15   -6.45 1.80e+00 3.09e-01 1.28e+01
  angle pdb=" C   LYS A 190 "
        pdb=" N   GLU A 191 "
        pdb=" CA  GLU A 191 "
      ideal   model   delta    sigma   weight residual
     122.56  116.69    5.87 1.72e+00 3.38e-01 1.16e+01
  angle pdb=" CA  TRP B 128 "
        pdb=" CB  TRP B 128 "
        pdb=" CG  TRP B 128 "
      ideal   model   delta    sigma   weight residual
     113.60  107.44    6.16 1.90e+00 2.77e-01 1.05e+01
  angle pdb=" N   GLN A 273 "
        pdb=" CA  GLN A 273 "
        pdb=" CB  GLN A 273 "
      ideal   model   delta    sigma   weight residual
     110.16  114.85   -4.69 1.48e+00 4.57e-01 1.00e+01
  angle pdb=" CB  GLN A 277 "
        pdb=" CG  GLN A 277 "
        pdb=" CD  GLN A 277 "
      ideal   model   delta    sigma   weight residual
     112.60  117.84   -5.24 1.70e+00 3.46e-01 9.50e+00
  ... (remaining 10625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 4148
       17.08 -    34.15: 438
       34.15 -    51.22: 65
       51.22 -    68.30: 11
       68.30 -    85.37: 8
  Dihedral angle restraints: 4670
    sinusoidal: 1861
      harmonic: 2809
  Sorted by residual:
  dihedral pdb=" CA  GLY C  80 "
           pdb=" C   GLY C  80 "
           pdb=" N   PHE C  81 "
           pdb=" CA  PHE C  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.94   21.06     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  ASP A 267 "
           pdb=" C   ASP A 267 "
           pdb=" N   ASP A 268 "
           pdb=" CA  ASP A 268 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.82  -20.18     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  ARG D 184 "
           pdb=" C   ARG D 184 "
           pdb=" N   GLY D 185 "
           pdb=" CA  GLY D 185 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.71   18.29     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 4667 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1104
       0.087 -    0.174: 120
       0.174 -    0.261: 4
       0.261 -    0.347: 0
       0.347 -    0.434: 1
  Chirality restraints: 1229
  Sorted by residual:
  chirality pdb=" CB  ILE A   6 "
            pdb=" CA  ILE A   6 "
            pdb=" CG1 ILE A   6 "
            pdb=" CG2 ILE A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.43 2.00e-01 2.50e+01 4.71e+00
  chirality pdb=" CB  ILE C  74 "
            pdb=" CA  ILE C  74 "
            pdb=" CG1 ILE C  74 "
            pdb=" CG2 ILE C  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  GLU A 191 "
            pdb=" N   GLU A 191 "
            pdb=" C   GLU A 191 "
            pdb=" CB  GLU A 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1226 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  97 "   -0.011 2.00e-02 2.50e+03   2.40e-02 1.01e+01
        pdb=" CG  PHE A  97 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  97 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  97 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  97 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  97 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  97 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 177 "    0.047 5.00e-02 4.00e+02   7.12e-02 8.11e+00
        pdb=" N   PRO B 178 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 178 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 178 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  72 "   -0.047 5.00e-02 4.00e+02   7.08e-02 8.03e+00
        pdb=" N   PRO B  73 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B  73 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B  73 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1738
        2.78 -     3.31: 7290
        3.31 -     3.84: 13828
        3.84 -     4.37: 16660
        4.37 -     4.90: 27732
  Nonbonded interactions: 67248
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 106 "
            pdb=" O   HOH A 301 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   LEU D 258 "
            pdb=" OG1 THR D 262 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OD2 ASP A 105 "
            pdb=" O   HOH A 302 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   PRO B 164 "
            pdb=" OH  TYR B 191 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG1 THR A  12 "
            pdb=" OD2 ASP A  60 "
     model   vdw
     2.315 3.040
  ... (remaining 67243 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.790
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:6.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
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      :  0.007   0.123   7850  Z= 0.263
  Angle     :  0.794   7.660  10630  Z= 0.431
  Chirality :  0.054   0.434   1229
  Planarity :  0.007   0.071   1327
  Dihedral  : 14.015  85.373   2860
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole: -0.65 (0.25), residues: 970
  helix: -0.32 (0.20), residues: 570
  sheet:  0.17 (0.63), residues: 61
  loop : -0.45 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 122 
 TYR   0.016   0.002   TYR C 134 
 PHE   0.050   0.003   PHE A  97 
 TRP   0.028   0.002   TRP B 128 
 HIS   0.004   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 ( 7850)
  covalent geometry    : angle       0.79421 (10630)
  hydrogen bonds       : bond        0.15892 (  445)
  hydrogen bonds       : angle       7.05324 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.321 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.5754
  time to fit residues: 97.7021
Evaluate side-chains
  122 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0010
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A 220 GLN
B   7 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.128455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.104440 restraints weight = 9767.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.59
r_work: 0.3050 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7850  Z= 0.135
  Angle     :  0.554   6.260  10630  Z= 0.295
  Chirality :  0.043   0.149   1229
  Planarity :  0.005   0.064   1327
  Dihedral  :  4.689  16.139   1038
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  8.53 %
    Favored  : 90.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.67 (0.26), residues: 970
  helix:  1.03 (0.22), residues: 563
  sheet: -0.29 (0.59), residues: 73
  loop : -0.24 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  20 
 TYR   0.014   0.001   TYR D 251 
 PHE   0.010   0.001   PHE C  55 
 TRP   0.021   0.001   TRP B 128 
 HIS   0.002   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7850)
  covalent geometry    : angle       0.55410 (10630)
  hydrogen bonds       : bond        0.04438 (  445)
  hydrogen bonds       : angle       4.88930 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  229 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7893 (pt0)
REVERT: A  271 LEU cc_start: 0.8637 (tp) cc_final: 0.8353 (tt)
REVERT: A  274 SER cc_start: 0.8197 (t) cc_final: 0.7483 (p)
REVERT: A  275 LEU cc_start: 0.8823 (mt) cc_final: 0.8584 (mt)
REVERT: B    7 ASN cc_start: 0.8173 (t0) cc_final: 0.7757 (t0)
REVERT: B  256 LEU cc_start: 0.8147 (mp) cc_final: 0.7944 (mp)
REVERT: C   33 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.6851 (tttm)
REVERT: C  168 SER cc_start: 0.8827 (m) cc_final: 0.8613 (p)
  outliers start: 11
  outliers final: 2
  residues processed: 142
  average time/residue: 0.5422
  time to fit residues: 81.4835
Evaluate side-chains
  135 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain C residue   33 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 73 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A  91 GLN
C  77 ASN
D 108 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.123774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.098606 restraints weight = 9758.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 1.70
r_work: 0.2955 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088   7850  Z= 0.279
  Angle     :  0.636   7.602  10630  Z= 0.333
  Chirality :  0.049   0.152   1229
  Planarity :  0.006   0.057   1327
  Dihedral  :  4.897  17.012   1038
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  9.74 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  0.82 (0.27), residues: 970
  helix:  1.16 (0.22), residues: 563
  sheet: -0.52 (0.62), residues: 62
  loop : -0.12 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 169 
 TYR   0.018   0.002   TYR C 134 
 PHE   0.014   0.002   PHE D 166 
 TRP   0.024   0.002   TRP B 128 
 HIS   0.004   0.001   HIS D  95 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 ( 7850)
  covalent geometry    : angle       0.63602 (10630)
  hydrogen bonds       : bond        0.05127 (  445)
  hydrogen bonds       : angle       4.91494 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 133
  time to evaluate  : 0.349 
Fit side-chains
REVERT: A  229 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7884 (pt0)
REVERT: A  277 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6880 (mp10)
REVERT: B    7 ASN cc_start: 0.8203 (t0) cc_final: 0.7782 (t0)
REVERT: B  130 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8652 (ttmt)
REVERT: B  163 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7628 (mp0)
REVERT: C   33 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.6910 (tttm)
REVERT: C   77 ASN cc_start: 0.7187 (t0) cc_final: 0.6979 (t0)
REVERT: C  107 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8528 (mt)
REVERT: C  168 SER cc_start: 0.8882 (m) cc_final: 0.8662 (p)
REVERT: D  142 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8514 (mtt)
REVERT: D  240 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7374 (mm-30)
  outliers start: 25
  outliers final: 7
  residues processed: 144
  average time/residue: 0.5365
  time to fit residues: 81.7310
Evaluate side-chains
  140 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  277 GLN
Chi-restraints excluded: chain B residue  130 LYS
Chi-restraints excluded: chain B residue  163 GLU
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   84 THR
Chi-restraints excluded: chain D residue  107 ILE
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  249 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 63 optimal weight:    0.4980
   chunk 47 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 92 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.126045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.100658 restraints weight = 9745.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.71
r_work: 0.2997 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7850  Z= 0.137
  Angle     :  0.528   6.540  10630  Z= 0.279
  Chirality :  0.043   0.149   1229
  Planarity :  0.005   0.055   1327
  Dihedral  :  4.514  15.555   1038
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 12.14 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.19 (0.27), residues: 970
  helix:  1.55 (0.22), residues: 566
  sheet: -0.59 (0.58), residues: 73
  loop : -0.09 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  20 
 TYR   0.014   0.001   TYR D 251 
 PHE   0.009   0.001   PHE A 231 
 TRP   0.020   0.002   TRP B 128 
 HIS   0.003   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7850)
  covalent geometry    : angle       0.52825 (10630)
  hydrogen bonds       : bond        0.04111 (  445)
  hydrogen bonds       : angle       4.62638 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.8541 (t0) cc_final: 0.8085 (t0)
REVERT: A  229 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7854 (pt0)
REVERT: C   33 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6996 (tttm)
REVERT: C  150 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7361 (mtm)
REVERT: D  142 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8426 (mtt)
REVERT: D  240 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7402 (mm-30)
  outliers start: 22
  outliers final: 7
  residues processed: 142
  average time/residue: 0.5334
  time to fit residues: 80.1599
Evaluate side-chains
  137 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue   14 ARG
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain C residue  150 MET
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  240 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0040
   chunk 90 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A  41 HIS
A  91 GLN
B   7 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.127406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.102253 restraints weight = 9658.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.67
r_work: 0.3024 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7850  Z= 0.124
  Angle     :  0.514   9.723  10630  Z= 0.268
  Chirality :  0.043   0.143   1229
  Planarity :  0.005   0.056   1327
  Dihedral  :  4.328  14.715   1038
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 13.22 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.35 (0.27), residues: 970
  helix:  1.73 (0.22), residues: 566
  sheet: -0.66 (0.58), residues: 73
  loop : -0.10 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.013   0.001   TYR D 251 
 PHE   0.008   0.001   PHE C  61 
 TRP   0.021   0.002   TRP A 276 
 HIS   0.003   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7850)
  covalent geometry    : angle       0.51448 (10630)
  hydrogen bonds       : bond        0.03864 (  445)
  hydrogen bonds       : angle       4.46693 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.8516 (t0) cc_final: 0.8068 (t0)
REVERT: A  229 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7844 (pt0)
REVERT: C   33 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.6987 (tttm)
REVERT: D   66 TRP cc_start: 0.7455 (t-100) cc_final: 0.6913 (t-100)
REVERT: D  142 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8373 (mtt)
REVERT: D  148 LEU cc_start: 0.7199 (pp) cc_final: 0.6849 (mm)
REVERT: D  240 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7453 (mm-30)
  outliers start: 23
  outliers final: 9
  residues processed: 146
  average time/residue: 0.5409
  time to fit residues: 83.5801
Evaluate side-chains
  137 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue   14 ARG
Chi-restraints excluded: chain C residue   33 LYS
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  249 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0970
   chunk 50 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0980
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A  41 HIS
A  91 GLN
A 202 HIS
B   7 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.129343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.104489 restraints weight = 9706.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.66
r_work: 0.3032 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7850  Z= 0.114
  Angle     :  0.505   8.674  10630  Z= 0.264
  Chirality :  0.042   0.151   1229
  Planarity :  0.005   0.055   1327
  Dihedral  :  4.205  15.073   1038
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 14.90 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.47 (0.27), residues: 970
  helix:  1.87 (0.22), residues: 565
  sheet: -0.57 (0.59), residues: 73
  loop : -0.15 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.012   0.001   TYR D 251 
 PHE   0.009   0.001   PHE C  61 
 TRP   0.023   0.001   TRP A 276 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7850)
  covalent geometry    : angle       0.50527 (10630)
  hydrogen bonds       : bond        0.03662 (  445)
  hydrogen bonds       : angle       4.38285 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.8499 (t0) cc_final: 0.8075 (t0)
REVERT: A  229 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7834 (pt0)
REVERT: D   66 TRP cc_start: 0.7464 (t-100) cc_final: 0.6940 (t-100)
REVERT: D  240 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7529 (mm-30)
  outliers start: 19
  outliers final: 6
  residues processed: 146
  average time/residue: 0.5730
  time to fit residues: 88.2832
Evaluate side-chains
  135 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 127
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  240 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0980
   chunk 83 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A  91 GLN
A 202 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.128579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.103593 restraints weight = 9713.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.66
r_work: 0.3041 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7850  Z= 0.120
  Angle     :  0.503   7.505  10630  Z= 0.265
  Chirality :  0.042   0.140   1229
  Planarity :  0.005   0.057   1327
  Dihedral  :  4.156  14.500   1038
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.90 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.58 (0.27), residues: 970
  helix:  1.93 (0.22), residues: 565
  sheet: -0.47 (0.59), residues: 73
  loop : -0.05 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A  20 
 TYR   0.013   0.001   TYR D 251 
 PHE   0.009   0.001   PHE C  61 
 TRP   0.026   0.001   TRP A 276 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7850)
  covalent geometry    : angle       0.50294 (10630)
  hydrogen bonds       : bond        0.03687 (  445)
  hydrogen bonds       : angle       4.35230 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.8483 (t0) cc_final: 0.8079 (t0)
REVERT: A  229 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7836 (pt0)
REVERT: A  276 TRP cc_start: 0.7131 (t-100) cc_final: 0.6652 (t60)
REVERT: B  246 GLU cc_start: 0.7865 (mp0) cc_final: 0.7637 (mp0)
REVERT: C  171 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8638 (mtpt)
REVERT: D   66 TRP cc_start: 0.7414 (t-100) cc_final: 0.6676 (t-100)
REVERT: D  142 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8402 (mtt)
REVERT: D  240 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7489 (mm-30)
  outliers start: 17
  outliers final: 7
  residues processed: 140
  average time/residue: 0.5491
  time to fit residues: 81.4166
Evaluate side-chains
  135 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain C residue   14 ARG
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  240 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A  91 GLN
A 163 GLN
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.125928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.100675 restraints weight = 9773.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 1.72
r_work: 0.3012 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2885 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   7850  Z= 0.182
  Angle     :  0.562   9.130  10630  Z= 0.293
  Chirality :  0.045   0.145   1229
  Planarity :  0.005   0.054   1327
  Dihedral  :  4.364  15.367   1038
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.90 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.45 (0.27), residues: 970
  helix:  1.76 (0.22), residues: 566
  sheet: -0.39 (0.59), residues: 73
  loop : -0.02 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.016   0.002   TYR D 251 
 PHE   0.011   0.002   PHE C 162 
 TRP   0.018   0.002   TRP B 128 
 HIS   0.003   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 7850)
  covalent geometry    : angle       0.56236 (10630)
  hydrogen bonds       : bond        0.04227 (  445)
  hydrogen bonds       : angle       4.52840 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.8524 (t0) cc_final: 0.8092 (t0)
REVERT: A  229 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7871 (pt0)
REVERT: A  269 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7652 (pm20)
REVERT: B  135 LYS cc_start: 0.8084 (mptt) cc_final: 0.6949 (mmmt)
REVERT: B  246 GLU cc_start: 0.7917 (mp0) cc_final: 0.7669 (mp0)
REVERT: D  142 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8434 (mtt)
REVERT: D  240 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7455 (mm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 142
  average time/residue: 0.5841
  time to fit residues: 87.4170
Evaluate side-chains
  144 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 GLU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain C residue   14 ARG
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  249 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 70 optimal weight:    5.9990
   chunk 94 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 7 optimal weight:    0.3980
   chunk 82 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A  41 HIS
A  91 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.128728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.103807 restraints weight = 9687.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.65
r_work: 0.3029 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7850  Z= 0.116
  Angle     :  0.509   9.162  10630  Z= 0.267
  Chirality :  0.042   0.139   1229
  Planarity :  0.005   0.055   1327
  Dihedral  :  4.188  14.272   1038
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.38 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.57 (0.27), residues: 970
  helix:  1.92 (0.22), residues: 565
  sheet: -0.51 (0.59), residues: 73
  loop : -0.05 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.019   0.001   TYR C  53 
 PHE   0.009   0.001   PHE C  61 
 TRP   0.032   0.002   TRP A 276 
 HIS   0.002   0.000   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7850)
  covalent geometry    : angle       0.50905 (10630)
  hydrogen bonds       : bond        0.03673 (  445)
  hydrogen bonds       : angle       4.39328 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.8503 (t0) cc_final: 0.8098 (t0)
REVERT: A  229 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7857 (pt0)
REVERT: A  269 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7677 (pm20)
REVERT: B  135 LYS cc_start: 0.7996 (mptt) cc_final: 0.6971 (mmmt)
REVERT: C   11 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7712 (mp)
REVERT: D   66 TRP cc_start: 0.7437 (t-100) cc_final: 0.6731 (t-100)
REVERT: D  142 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8389 (mtt)
REVERT: D  240 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7485 (mm-30)
  outliers start: 18
  outliers final: 10
  residues processed: 145
  average time/residue: 0.5590
  time to fit residues: 85.4756
Evaluate side-chains
  145 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 GLU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   14 ARG
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  249 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A  91 GLN
A 202 HIS
** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.102555 restraints weight = 9733.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 1.71
r_work: 0.3016 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7850  Z= 0.146
  Angle     :  0.541   9.207  10630  Z= 0.282
  Chirality :  0.043   0.138   1229
  Planarity :  0.005   0.055   1327
  Dihedral  :  4.244  15.537   1038
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.87 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.56 (0.27), residues: 970
  helix:  1.89 (0.22), residues: 565
  sheet: -0.47 (0.59), residues: 73
  loop : -0.01 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.014   0.001   TYR D 251 
 PHE   0.008   0.001   PHE A 231 
 TRP   0.028   0.002   TRP A 276 
 HIS   0.003   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 7850)
  covalent geometry    : angle       0.54053 (10630)
  hydrogen bonds       : bond        0.03900 (  445)
  hydrogen bonds       : angle       4.43765 ( 1287)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 ASN cc_start: 0.8511 (t0) cc_final: 0.8092 (t0)
REVERT: A  229 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7876 (pt0)
REVERT: A  269 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7642 (pm20)
REVERT: B  135 LYS cc_start: 0.7933 (mptt) cc_final: 0.6898 (mmmt)
REVERT: D   66 TRP cc_start: 0.7389 (t-100) cc_final: 0.6915 (t-100)
REVERT: D  142 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8406 (mtt)
REVERT: D  240 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7456 (mm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 144
  average time/residue: 0.5914
  time to fit residues: 89.9482
Evaluate side-chains
  146 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 PHE
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  268 ASP
Chi-restraints excluded: chain A residue  269 GLU
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  187 LEU
Chi-restraints excluded: chain C residue   14 ARG
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  240 GLU
Chi-restraints excluded: chain D residue  249 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0670
   chunk 69 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A  41 HIS
A  91 GLN
A 202 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.128370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.103414 restraints weight = 9588.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.66
r_work: 0.3012 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7850  Z= 0.126
  Angle     :  0.527   9.574  10630  Z= 0.274
  Chirality :  0.043   0.138   1229
  Planarity :  0.005   0.056   1327
  Dihedral  :  4.193  15.199   1038
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.99 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 are not related in a simple way.
  whole:  1.57 (0.27), residues: 970
  helix:  1.92 (0.22), residues: 565
  sheet: -0.54 (0.59), residues: 73
  loop : -0.03 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  20 
 TYR   0.013   0.001   TYR D 251 
 PHE   0.008   0.001   PHE C  61 
 TRP   0.027   0.002   TRP A 276 
 HIS   0.002   0.000   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7850)
  covalent geometry    : angle       0.52665 (10630)
  hydrogen bonds       : bond        0.03742 (  445)
  hydrogen bonds       : angle       4.40435 ( 1287)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3019.44 seconds
wall clock time: 52 minutes 2.29 seconds (3122.29 seconds total)