Starting phenix.real_space_refine
on Wed Feb 12 19:45:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s8m_24897/02_2025/7s8m_24897.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8m_24897/02_2025/7s8m_24897.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s8m_24897/02_2025/7s8m_24897.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8m_24897/02_2025/7s8m_24897.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8m_24897/02_2025/7s8m_24897.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8m_24897/02_2025/7s8m_24897.cif"
  }
  resolution = 2.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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      63      5.16       5
     C    5343      2.51       5
     N    1408      2.21       5
     O    1532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8346
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1707
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 2564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2564
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "D"
      Number of atoms: 401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 401
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 1743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1743
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "R"
      Number of atoms: 1892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1892
          Classifications: {'peptide': 253}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 8, 'TRANS': 244}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 134
          Unresolved non-hydrogen angles: 170
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 7, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 84
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 39
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 5.31, per 1000 atoms: 0.64
  Number of scatterers: 8346
  At special positions: 0
  Unit cell: (102.08, 117.92, 117.92, 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      63     16.00
     O    1532      8.00
     N    1408      7.00
     C    5343      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 168 " - pdb=" SG  CYS R 180 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 977.8 milliseconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      36.9% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 4.667A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 5.719A  pdb=" N   HIS B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
    Processing helix  chain 'B' and resid 270 through 281
      removed outlier: 4.144A  pdb=" N   LYS B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   LYS B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.541A  pdb=" N   ILE B 285 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 310
      removed outlier: 3.683A  pdb=" N   LEU B 310 " --> pdb=" O   GLN B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 351
      removed outlier: 3.633A  pdb=" N   ASP B 341 " --> pdb=" O   ASP B 337 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 342 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 24
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.501A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 55 through 59
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.823A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 57
      removed outlier: 3.966A  pdb=" N   VAL R  34 " --> pdb=" O   THR R  30 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL R  43 " --> pdb=" O   PHE R  39 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLY R  44 " --> pdb=" O   ILE R  40 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   PHE R  57 " --> pdb=" O   TRP R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 64 through 95
      removed outlier: 3.779A  pdb=" N   VAL R  68 " --> pdb=" O   PHE R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 103 through 133
      removed outlier: 3.874A  pdb=" N   THR R 107 " --> pdb=" O   SER R 103 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL R 108 " --> pdb=" O   PHE R 104 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LEU R 120 " --> pdb=" O   GLY R 116 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   SER R 121 " --> pdb=" O   LEU R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 139
    Processing helix  chain 'R' and resid 144 through 167
    Processing helix  chain 'R' and resid 177 through 212
    Processing helix  chain 'R' and resid 217 through 236
    Processing helix  chain 'R' and resid 236 through 250
      removed outlier: 4.291A  pdb=" N   GLY R 240 " --> pdb=" O   GLY R 236 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   LEU R 247 " --> pdb=" O   TRP R 243 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   TRP R 248 " --> pdb=" O   PHE R 244 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 257 through 280
      Proline residue:  R 262  - end of helix
      Proline residue:  R 276  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190
    Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51
      removed outlier: 6.293A  pdb=" N   THR C  47 " --> pdb=" O   ASN C 340 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   ASN C 340 " --> pdb=" O   THR C  47 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.826A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.430A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.908A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.585A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.992A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.522A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.554A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.996A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.996A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136
      removed outlier: 6.338A  pdb=" N   VAL E 135 " --> pdb=" O   GLU E 234 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1239 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2666
        1.34 -     1.46: 1967
        1.46 -     1.58: 3802
        1.58 -     1.69: 0
        1.69 -     1.81: 87
  Bond restraints: 8522
  Sorted by residual:
  bond pdb=" CB  ASP R  75 "
       pdb=" CG  ASP R  75 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.37e+00
  bond pdb=" CG1 ILE C  58 "
       pdb=" CD1 ILE C  58 "
    ideal  model  delta    sigma   weight residual
    1.513  1.470  0.043 3.90e-02 6.57e+02 1.22e+00
  bond pdb=" CG  LEU R 237 "
       pdb=" CD1 LEU R 237 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 1.02e+00
  bond pdb=" C   GLU E 222 "
       pdb=" N   TYR E 223 "
    ideal  model  delta    sigma   weight residual
    1.330  1.318  0.012 1.47e-02 4.63e+03 7.05e-01
  bond pdb=" CG  LEU R  45 "
       pdb=" CD2 LEU R  45 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.66e-01
  ... (remaining 8517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 11209
        1.41 -     2.81: 294
        2.81 -     4.22: 48
        4.22 -     5.63: 17
        5.63 -     7.04: 5
  Bond angle restraints: 11573
  Sorted by residual:
  angle pdb=" N   PRO E 224 "
        pdb=" CA  PRO E 224 "
        pdb=" C   PRO E 224 "
      ideal   model   delta    sigma   weight residual
     112.10  118.27   -6.17 2.60e+00 1.48e-01 5.64e+00
  angle pdb=" N   GLY B 352 "
        pdb=" CA  GLY B 352 "
        pdb=" C   GLY B 352 "
      ideal   model   delta    sigma   weight residual
     114.67  117.97   -3.30 1.41e+00 5.03e-01 5.47e+00
  angle pdb=" N   ASP C 291 "
        pdb=" CA  ASP C 291 "
        pdb=" C   ASP C 291 "
      ideal   model   delta    sigma   weight residual
     112.97  110.60    2.37 1.06e+00 8.90e-01 5.01e+00
  angle pdb=" CA  TYR E 178 "
        pdb=" CB  TYR E 178 "
        pdb=" CG  TYR E 178 "
      ideal   model   delta    sigma   weight residual
     113.90  117.79   -3.89 1.80e+00 3.09e-01 4.66e+00
  angle pdb=" CA  ARG E 206 "
        pdb=" CB  ARG E 206 "
        pdb=" CG  ARG E 206 "
      ideal   model   delta    sigma   weight residual
     114.10  118.19   -4.09 2.00e+00 2.50e-01 4.19e+00
  ... (remaining 11568 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 4587
       16.95 -    33.89: 316
       33.89 -    50.84: 68
       50.84 -    67.78: 11
       67.78 -    84.73: 5
  Dihedral angle restraints: 4987
    sinusoidal: 1808
      harmonic: 3179
  Sorted by residual:
  dihedral pdb=" CA  ARG E 179 "
           pdb=" C   ARG E 179 "
           pdb=" N   MET E 180 "
           pdb=" CA  MET E 180 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.06  -25.94     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASN B 347 "
           pdb=" C   ASN B 347 "
           pdb=" N   LEU B 348 "
           pdb=" CA  LEU B 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.57   22.43     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  PHE C 234 "
           pdb=" C   PHE C 234 "
           pdb=" N   PHE C 235 "
           pdb=" CA  PHE C 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.41   19.59     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 4984 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 838
       0.033 -    0.066: 344
       0.066 -    0.099: 105
       0.099 -    0.133: 49
       0.133 -    0.166: 8
  Chirality restraints: 1344
  Sorted by residual:
  chirality pdb=" CA  TYR E 178 "
            pdb=" N   TYR E 178 "
            pdb=" C   TYR E 178 "
            pdb=" CB  TYR E 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.87e-01
  chirality pdb=" CA  VAL E  37 "
            pdb=" N   VAL E  37 "
            pdb=" C   VAL E  37 "
            pdb=" CB  VAL E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  PRO E 224 "
            pdb=" N   PRO E 224 "
            pdb=" C   PRO E 224 "
            pdb=" CB  PRO E 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.49e-01
  ... (remaining 1341 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 129 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" C   LEU R 129 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LEU R 129 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER R 130 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 242 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   GLN R 242 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLN R 242 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   TRP R 243 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 123 "   -0.008 2.00e-02 2.50e+03   1.61e-02 2.58e+00
        pdb=" C   VAL R 123 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL R 123 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER R 124 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 268
        2.72 -     3.26: 8118
        3.26 -     3.81: 13659
        3.81 -     4.35: 16864
        4.35 -     4.90: 29665
  Nonbonded interactions: 68574
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B  14 "
            pdb=" OG1 THR E  57 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER C 281 "
            pdb=" OD2 ASP D  48 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG1 THR C 274 "
            pdb=" O   VAL C 315 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   CYS B 254 "
            pdb=" NZ  LYS B 317 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OD1 ASP B 272 "
            pdb=" N   LEU B 273 "
     model   vdw
     2.249 3.120
  ... (remaining 68569 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:             1.880
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.430
  Find NCS groups from input model:        0.100
  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:11.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
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   0.043   8522  Z= 0.240
  Angle     :  0.589   7.037  11573  Z= 0.326
  Chirality :  0.043   0.166   1344
  Planarity :  0.004   0.031   1452
  Dihedral  : 12.635  84.726   2932
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.26), residues: 1082
  helix:  2.00 (0.28), residues: 369
  sheet:  0.15 (0.29), residues: 276
  loop : -1.08 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  82 
 HIS   0.004   0.001   HIS C 142 
 PHE   0.019   0.002   PHE B 189 
 TYR   0.018   0.002   TYR E 178 
 ARG   0.003   0.000   ARG C 219 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: B   17 LYS cc_start: 0.7754 (mmtp) cc_final: 0.7523 (mmtp)
REVERT: C   25 CYS cc_start: 0.7535 (p) cc_final: 0.7145 (p)
REVERT: C  254 ASP cc_start: 0.7040 (t70) cc_final: 0.6791 (t0)
REVERT: R  109 MET cc_start: 0.6736 (ttp) cc_final: 0.6462 (ttm)
REVERT: R  280 PHE cc_start: 0.7849 (t80) cc_final: 0.7147 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.9714
  time to fit residues: 210.3866
Evaluate side-chains
  183 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 50 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 255 ASN
C  75 GLN
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.131561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.117081 restraints weight = 11002.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 1.62
r_work: 0.3498 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8522  Z= 0.241
  Angle     :  0.565   7.782  11573  Z= 0.297
  Chirality :  0.043   0.152   1344
  Planarity :  0.003   0.031   1452
  Dihedral  :  4.482  24.683   1173
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.35 %
    Favored  : 90.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1082
  helix:  2.65 (0.28), residues: 373
  sheet:  0.37 (0.29), residues: 275
  loop : -1.05 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R 243 
 HIS   0.003   0.001   HIS C 142 
 PHE   0.018   0.002   PHE B 189 
 TYR   0.020   0.002   TYR E 178 
 ARG   0.002   0.000   ARG C 197 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 192
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: B  249 LEU cc_start: 0.8430 (tt) cc_final: 0.8229 (tt)
REVERT: C   25 CYS cc_start: 0.7907 (p) cc_final: 0.7528 (p)
REVERT: C  197 ARG cc_start: 0.7788 (mmt180) cc_final: 0.7545 (mmt180)
REVERT: E   30 SER cc_start: 0.8242 (m) cc_final: 0.8027 (t)
REVERT: R   45 LEU cc_start: 0.7581 (mm) cc_final: 0.7190 (mm)
REVERT: R  280 PHE cc_start: 0.8174 (t80) cc_final: 0.7700 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 196
  average time/residue: 0.9491
  time to fit residues: 200.9510
Evaluate side-chains
  192 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 184
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0770
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
C 220 GLN
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.131426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.116880 restraints weight = 11157.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 1.66
r_work: 0.3497 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8522  Z= 0.214
  Angle     :  0.530   6.622  11573  Z= 0.280
  Chirality :  0.042   0.151   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.332  23.964   1173
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.10 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.26), residues: 1082
  helix:  2.75 (0.28), residues: 375
  sheet:  0.32 (0.29), residues: 279
  loop : -0.96 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.018   0.001   PHE B 189 
 TYR   0.018   0.002   TYR E 178 
 ARG   0.002   0.000   ARG R 127 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8256 (mtmm)
REVERT: C   25 CYS cc_start: 0.7933 (p) cc_final: 0.7523 (p)
REVERT: C  197 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7566 (mmt180)
REVERT: C  217 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8266 (pmm)
REVERT: C  258 ASP cc_start: 0.7431 (t0) cc_final: 0.7132 (t0)
REVERT: E   30 SER cc_start: 0.8296 (m) cc_final: 0.8041 (t)
REVERT: R   45 LEU cc_start: 0.7609 (mm) cc_final: 0.7229 (mm)
REVERT: R  280 PHE cc_start: 0.8213 (t80) cc_final: 0.7739 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 198
  average time/residue: 0.9452
  time to fit residues: 202.2087
Evaluate side-chains
  202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 49 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 269 ASN
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.130572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.116141 restraints weight = 11022.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 1.62
r_work: 0.3488 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8522  Z= 0.262
  Angle     :  0.547   7.283  11573  Z= 0.287
  Chirality :  0.043   0.159   1344
  Planarity :  0.003   0.033   1452
  Dihedral  :  4.372  24.544   1173
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 11.33 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1082
  helix:  2.77 (0.27), residues: 375
  sheet:  0.25 (0.30), residues: 271
  loop : -1.03 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  82 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.018   0.002   PHE B 189 
 TYR   0.020   0.002   TYR E 178 
 ARG   0.003   0.000   ARG R 127 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 184
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8265 (mtmm)
REVERT: C   25 CYS cc_start: 0.7936 (p) cc_final: 0.7524 (p)
REVERT: C  197 ARG cc_start: 0.7829 (mmt180) cc_final: 0.7545 (mmt180)
REVERT: C  217 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8249 (pmm)
REVERT: E   30 SER cc_start: 0.8272 (m) cc_final: 0.8044 (t)
REVERT: R   45 LEU cc_start: 0.7596 (mm) cc_final: 0.7185 (mm)
REVERT: R  280 PHE cc_start: 0.8211 (t80) cc_final: 0.7733 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 196
  average time/residue: 0.9092
  time to fit residues: 193.1766
Evaluate side-chains
  201 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain D residue   38 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 92 optimal weight:    0.0980
   chunk 106 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0030
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.131852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.117410 restraints weight = 11074.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 1.65
r_work: 0.3505 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8522  Z= 0.194
  Angle     :  0.520   6.181  11573  Z= 0.274
  Chirality :  0.042   0.148   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.254  22.791   1173
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.62 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.26), residues: 1082
  helix:  2.93 (0.27), residues: 369
  sheet:  0.25 (0.30), residues: 272
  loop : -0.97 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.017   0.001   PHE B 189 
 TYR   0.017   0.001   TYR E 178 
 ARG   0.002   0.000   ARG R 127 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8257 (mtmm)
REVERT: C   25 CYS cc_start: 0.7934 (p) cc_final: 0.7516 (p)
REVERT: C  197 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7543 (mmt180)
REVERT: C  217 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8232 (pmm)
REVERT: E   30 SER cc_start: 0.8272 (m) cc_final: 0.8035 (t)
REVERT: R   45 LEU cc_start: 0.7609 (mm) cc_final: 0.7242 (mm)
REVERT: R  280 PHE cc_start: 0.8214 (t80) cc_final: 0.7743 (t80)
  outliers start: 21
  outliers final: 17
  residues processed: 192
  average time/residue: 0.9682
  time to fit residues: 200.6205
Evaluate side-chains
  197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 179
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 17 optimal weight:    0.0970
   chunk 87 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 57 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 24 optimal weight:    0.1980
   chunk 54 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.131318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.116543 restraints weight = 11218.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.66
r_work: 0.3520 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8522  Z= 0.182
  Angle     :  0.510   5.851  11573  Z= 0.269
  Chirality :  0.041   0.142   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.174  21.394   1173
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.39 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1082
  helix:  2.99 (0.27), residues: 369
  sheet:  0.27 (0.30), residues: 277
  loop : -0.91 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 189 
 TYR   0.017   0.001   TYR E 178 
 ARG   0.002   0.000   ARG R 127 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: B  271 LYS cc_start: 0.7986 (ptmm) cc_final: 0.7650 (ptmm)
REVERT: B  279 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8277 (mtmm)
REVERT: C   25 CYS cc_start: 0.7972 (p) cc_final: 0.7557 (p)
REVERT: C  197 ARG cc_start: 0.7827 (mmt180) cc_final: 0.7576 (mmt180)
REVERT: C  217 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8199 (pmm)
REVERT: E   30 SER cc_start: 0.8238 (m) cc_final: 0.8035 (t)
REVERT: R   45 LEU cc_start: 0.7614 (mm) cc_final: 0.7236 (mm)
REVERT: R  280 PHE cc_start: 0.8201 (t80) cc_final: 0.7712 (t80)
  outliers start: 25
  outliers final: 16
  residues processed: 190
  average time/residue: 0.9768
  time to fit residues: 200.4944
Evaluate side-chains
  193 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 176
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  227 SER
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9990
   chunk 87 optimal weight:    0.5980
   chunk 102 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.131151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.116336 restraints weight = 11193.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 1.66
r_work: 0.3518 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8522  Z= 0.196
  Angle     :  0.526   9.297  11573  Z= 0.272
  Chirality :  0.042   0.148   1344
  Planarity :  0.003   0.031   1452
  Dihedral  :  4.159  21.263   1173
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.53 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1082
  helix:  3.01 (0.27), residues: 369
  sheet:  0.33 (0.31), residues: 272
  loop : -0.87 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 189 
 TYR   0.017   0.002   TYR E 178 
 ARG   0.002   0.000   ARG R 127 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 179
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
REVERT: B  279 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8284 (mtmm)
REVERT: C   25 CYS cc_start: 0.7962 (p) cc_final: 0.7543 (p)
REVERT: C  146 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8472 (mt)
REVERT: C  197 ARG cc_start: 0.7787 (mmt180) cc_final: 0.7567 (mmt180)
REVERT: R   45 LEU cc_start: 0.7617 (mm) cc_final: 0.7253 (mm)
REVERT: R  280 PHE cc_start: 0.8197 (t80) cc_final: 0.7714 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 190
  average time/residue: 0.9346
  time to fit residues: 191.8379
Evaluate side-chains
  195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 178
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue   88 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 87 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0070
   chunk 75 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0570
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.2634

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
E 130 GLN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.132778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.117838 restraints weight = 11366.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.71
r_work: 0.3535 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8522  Z= 0.144
  Angle     :  0.504   8.872  11573  Z= 0.260
  Chirality :  0.041   0.138   1344
  Planarity :  0.003   0.030   1452
  Dihedral  :  4.002  20.213   1173
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.42 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1082
  helix:  3.09 (0.27), residues: 369
  sheet:  0.38 (0.31), residues: 271
  loop : -0.83 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.002   0.000   HIS E  35 
 PHE   0.015   0.001   PHE B 189 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.001   0.000   ARG C 251 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
REVERT: B  271 LYS cc_start: 0.8041 (ptmm) cc_final: 0.7730 (ptmm)
REVERT: C   25 CYS cc_start: 0.7943 (p) cc_final: 0.7523 (p)
REVERT: C  146 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8440 (mt)
REVERT: C  197 ARG cc_start: 0.7858 (mmt180) cc_final: 0.7638 (mmt180)
REVERT: C  217 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8219 (pmm)
REVERT: R  280 PHE cc_start: 0.8188 (t80) cc_final: 0.7734 (t80)
  outliers start: 21
  outliers final: 15
  residues processed: 188
  average time/residue: 0.9602
  time to fit residues: 194.7880
Evaluate side-chains
  192 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   33 ILE
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 99 optimal weight:    0.5980
   chunk 101 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0970
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 220 GLN
C 239 ASN
C 268 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.131022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.116204 restraints weight = 11303.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 1.67
r_work: 0.3517 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8522  Z= 0.227
  Angle     :  0.540   9.051  11573  Z= 0.279
  Chirality :  0.042   0.149   1344
  Planarity :  0.003   0.033   1452
  Dihedral  :  4.150  20.220   1173
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.22 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1082
  helix:  3.10 (0.27), residues: 369
  sheet:  0.33 (0.30), residues: 266
  loop : -0.84 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 189 
 TYR   0.019   0.002   TYR E 178 
 ARG   0.009   0.000   ARG C 129 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: B  197 LYS cc_start: 0.8705 (mttm) cc_final: 0.8486 (mttm)
REVERT: B  279 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8288 (mtmm)
REVERT: C   25 CYS cc_start: 0.7965 (p) cc_final: 0.7538 (p)
REVERT: C  197 ARG cc_start: 0.7828 (mmt180) cc_final: 0.7589 (mmt180)
  outliers start: 20
  outliers final: 18
  residues processed: 191
  average time/residue: 0.9427
  time to fit residues: 194.3484
Evaluate side-chains
  195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 74 optimal weight:    0.1980
   chunk 105 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 96 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 220 GLN
C 268 ASN
C 340 ASN
E 182 ASN
R  48 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.130643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.115868 restraints weight = 11258.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.66
r_work: 0.3513 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3373 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8522  Z= 0.226
  Angle     :  0.539   9.014  11573  Z= 0.279
  Chirality :  0.042   0.150   1344
  Planarity :  0.003   0.033   1452
  Dihedral  :  4.191  20.944   1173
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.45 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1082
  helix:  3.08 (0.27), residues: 368
  sheet:  0.32 (0.31), residues: 267
  loop : -0.87 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.001   PHE B 189 
 TYR   0.019   0.002   TYR E 178 
 ARG   0.009   0.000   ARG C 129 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: B  197 LYS cc_start: 0.8701 (mttm) cc_final: 0.8484 (mttm)
REVERT: C   25 CYS cc_start: 0.7959 (p) cc_final: 0.7542 (p)
REVERT: C  197 ARG cc_start: 0.7831 (mmt180) cc_final: 0.7602 (mmt180)
REVERT: R  280 PHE cc_start: 0.8115 (t80) cc_final: 0.7800 (t80)
  outliers start: 18
  outliers final: 18
  residues processed: 187
  average time/residue: 0.9982
  time to fit residues: 201.3953
Evaluate side-chains
  194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 176
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  165 THR
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain D residue   21 MET
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  183 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain R residue   66 VAL
Chi-restraints excluded: chain R residue  131 VAL
Chi-restraints excluded: chain R residue  168 CYS
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  277 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 39 optimal weight:    0.0050
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 99 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 91 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
C 268 ASN
R  48 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.130970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.116139 restraints weight = 11389.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.67
r_work: 0.3513 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8522  Z= 0.213
  Angle     :  0.544   8.865  11573  Z= 0.281
  Chirality :  0.042   0.152   1344
  Planarity :  0.003   0.032   1452
  Dihedral  :  4.180  20.752   1173
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.56 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.26), residues: 1082
  helix:  3.01 (0.27), residues: 369
  sheet:  0.29 (0.31), residues: 267
  loop : -0.88 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.018   0.001   PHE R 280 
 TYR   0.018   0.002   TYR E 178 
 ARG   0.008   0.000   ARG C 129 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6788.15 seconds
wall clock time: 120 minutes 31.78 seconds (7231.78 seconds total)