Starting phenix.real_space_refine
on Tue Apr 29 02:51:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z3m_39747/04_2025/8z3m_39747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z3m_39747/04_2025/8z3m_39747.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z3m_39747/04_2025/8z3m_39747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z3m_39747/04_2025/8z3m_39747.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z3m_39747/04_2025/8z3m_39747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z3m_39747/04_2025/8z3m_39747.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
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      46      5.16       5
     C    5379      2.51       5
     N    1433      2.21       5
     O    1537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8395
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1783
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 203
          Unresolved non-hydrogen dihedrals: 134
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 118
    Chain: "B"
      Number of atoms: 2458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2458
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 10, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 96
    Chain: "G"
      Number of atoms: 334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 334
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "S"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1662
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 134
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 4, 'PHE:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 80
    Chain: "R"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2158
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 51}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 279}
          Unresolved non-hydrogen bonds: 207
          Unresolved non-hydrogen angles: 253
          Unresolved non-hydrogen dihedrals: 174
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 145
  Time building chain proxies: 5.14, per 1000 atoms: 0.61
  Number of scatterers: 8395
  At special positions: 0
  Unit cell: (94.3, 119.72, 127.1, 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      46     16.00
     O    1537      8.00
     N    1433      7.00
     C    5379      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  90 " - pdb=" SG  CYS R 168 " 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 1.0 seconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      38.3% alpha, 21.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.586A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 57
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 3.866A  pdb=" N   ASN A 214 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 243
    Processing helix  chain 'A' and resid 259 through 268
    Processing helix  chain 'A' and resid 272 through 276
    Processing helix  chain 'A' and resid 277 through 281
      removed outlier: 3.814A  pdb=" N   ALA A 281 " --> pdb=" O   PRO A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 317
      removed outlier: 3.556A  pdb=" N   GLU A 309 " --> pdb=" O   PHE A 305 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   SER A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 12 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 4.088A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.107A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'R' and resid 18 through 48
      removed outlier: 3.553A  pdb=" N   SER R  22 " --> pdb=" O   LEU R  18 " (cutoff:3.500A)
      Proline residue:  R  33  - end of helix
    Processing helix  chain 'R' and resid 50 through 79
      removed outlier: 4.095A  pdb=" N   VAL R  54 " --> pdb=" O   ASN R  50 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR R  55 " --> pdb=" O   GLU R  51 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 86 through 94
    Processing helix  chain 'R' and resid 94 through 120
      removed outlier: 4.414A  pdb=" N   ILE R 101 " --> pdb=" O   PHE R  97 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR R 102 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 129
    Processing helix  chain 'R' and resid 130 through 149
      removed outlier: 3.568A  pdb=" N   ASN R 149 " --> pdb=" O   GLU R 145 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 150 through 155
      removed outlier: 3.677A  pdb=" N   PHE R 154 " --> pdb=" O   SER R 150 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   HIS R 155 " --> pdb=" O   ALA R 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 150 through 155'
    Processing helix  chain 'R' and resid 175 through 188
    Processing helix  chain 'R' and resid 190 through 210
    Processing helix  chain 'R' and resid 215 through 254
      Proline residue:  R 239  - end of helix
    Processing helix  chain 'R' and resid 258 through 275
      removed outlier: 3.715A  pdb=" N   GLU R 262 " --> pdb=" O   CYS R 258 " (cutoff:3.500A)
      removed outlier: 4.986A  pdb=" N   SER R 266 " --> pdb=" O   GLU R 262 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   ALA R 267 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 277 through 288
      Proline residue:  R 283  - end of helix
    Processing helix  chain 'R' and resid 290 through 300
      removed outlier: 3.623A  pdb=" N   ARG R 294 " --> pdb=" O   ASN R 290 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 189
      removed outlier: 6.740A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   PHE A 197 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   VAL A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 218 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   ILE A 220 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   VAL A 222 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   ASP A 224 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ILE A 219 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 255 " --> pdb=" O   ILE A 219 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   PHE A 221 " --> pdb=" O   PHE A 255 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ASN A 257 " --> pdb=" O   PHE A 221 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   VAL A 223 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.581A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.835A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.012A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.535A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.880A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.635A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.754A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.696A  pdb=" N   THR S 118 " --> pdb=" O   GLY S  10 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130
    Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136
      removed outlier: 4.205A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE S 177 " --> pdb=" O   TRP S 164 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   LEU S 166 " --> pdb=" O   LEU S 175 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   LEU S 175 " --> pdb=" O   LEU S 166 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1245 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: 2.50

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1348
        1.29 -     1.42: 2372
        1.42 -     1.55: 4808
        1.55 -     1.69: 0
        1.69 -     1.82: 64
  Bond restraints: 8592
  Sorted by residual:
  bond pdb=" C   PHE R 159 "
       pdb=" O   PHE R 159 "
    ideal  model  delta    sigma   weight residual
    1.236  1.157  0.079 1.14e-02 7.69e+03 4.76e+01
  bond pdb=" CA  ALA R 249 "
       pdb=" C   ALA R 249 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.081 1.26e-02 6.30e+03 4.18e+01
  bond pdb=" CA  TRP R  83 "
       pdb=" C   TRP R  83 "
    ideal  model  delta    sigma   weight residual
    1.524  1.444  0.079 1.30e-02 5.92e+03 3.71e+01
  bond pdb=" N   ILE R  84 "
       pdb=" CA  ILE R  84 "
    ideal  model  delta    sigma   weight residual
    1.459  1.389  0.070 1.25e-02 6.40e+03 3.10e+01
  bond pdb=" CA  TYR R 251 "
       pdb=" C   TYR R 251 "
    ideal  model  delta    sigma   weight residual
    1.523  1.451  0.072 1.30e-02 5.92e+03 3.06e+01
  ... (remaining 8587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 11602
        2.70 -     5.40: 123
        5.40 -     8.09: 9
        8.09 -    10.79: 4
       10.79 -    13.49: 3
  Bond angle restraints: 11741
  Sorted by residual:
  angle pdb=" N   ASN R 164 "
        pdb=" CA  ASN R 164 "
        pdb=" C   ASN R 164 "
      ideal   model   delta    sigma   weight residual
     112.47  124.79  -12.32 1.24e+00 6.50e-01 9.88e+01
  angle pdb=" N   HIS R  79 "
        pdb=" CA  HIS R  79 "
        pdb=" C   HIS R  79 "
      ideal   model   delta    sigma   weight residual
     110.59   99.39   11.20 1.45e+00 4.76e-01 5.97e+01
  angle pdb=" N   TYR R 163 "
        pdb=" CA  TYR R 163 "
        pdb=" C   TYR R 163 "
      ideal   model   delta    sigma   weight residual
     110.68  120.36   -9.68 1.39e+00 5.18e-01 4.85e+01
  angle pdb=" N   ILE R  84 "
        pdb=" CA  ILE R  84 "
        pdb=" C   ILE R  84 "
      ideal   model   delta    sigma   weight residual
     109.34   95.85   13.49 2.08e+00 2.31e-01 4.20e+01
  angle pdb=" N   LYS A 270 "
        pdb=" CA  LYS A 270 "
        pdb=" C   LYS A 270 "
      ideal   model   delta    sigma   weight residual
     113.40  122.74   -9.34 1.47e+00 4.63e-01 4.04e+01
  ... (remaining 11736 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.20: 4464
       15.20 -    30.41: 403
       30.41 -    45.61: 90
       45.61 -    60.82: 12
       60.82 -    76.02: 8
  Dihedral angle restraints: 4977
    sinusoidal: 1644
      harmonic: 3333
  Sorted by residual:
  dihedral pdb=" N   LYS A 270 "
           pdb=" C   LYS A 270 "
           pdb=" CA  LYS A 270 "
           pdb=" CB  LYS A 270 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.69  -15.89     0      2.50e+00 1.60e-01 4.04e+01
  dihedral pdb=" C   LYS A 270 "
           pdb=" N   LYS A 270 "
           pdb=" CA  LYS A 270 "
           pdb=" CB  LYS A 270 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.84   15.24     0      2.50e+00 1.60e-01 3.72e+01
  dihedral pdb=" CB  CYS S 147 "
           pdb=" SG  CYS S 147 "
           pdb=" SG  CYS S 217 "
           pdb=" CB  CYS S 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  131.33  -38.33     1      1.00e+01 1.00e-02 2.07e+01
  ... (remaining 4974 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.151: 1351
       0.151 -    0.302: 12
       0.302 -    0.453: 1
       0.453 -    0.603: 2
       0.603 -    0.754: 1
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" CA  LYS A 270 "
            pdb=" N   LYS A 270 "
            pdb=" C   LYS A 270 "
            pdb=" CB  LYS A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CA  TYR R 163 "
            pdb=" N   TYR R 163 "
            pdb=" C   TYR R 163 "
            pdb=" CB  TYR R 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.38e+00
  chirality pdb=" CA  ASN R 164 "
            pdb=" N   ASN R 164 "
            pdb=" C   ASN R 164 "
            pdb=" CB  ASN R 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.97    0.54 2.00e-01 2.50e+01 7.24e+00
  ... (remaining 1364 not shown)

  Planarity restraints: 1496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  78 "    0.013 2.00e-02 2.50e+03   2.76e-02 7.62e+00
        pdb=" C   LEU R  78 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU R  78 "    0.018 2.00e-02 2.50e+03
        pdb=" N   HIS R  79 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET R 181 "   -0.012 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   MET R 181 "    0.044 2.00e-02 2.50e+03
        pdb=" O   MET R 181 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASN R 182 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL S  64 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.87e+00
        pdb=" C   VAL S  64 "    0.042 2.00e-02 2.50e+03
        pdb=" O   VAL S  64 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LYS S  65 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1493 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 33
        2.47 -     3.08: 5810
        3.08 -     3.69: 13056
        3.69 -     4.29: 18809
        4.29 -     4.90: 31468
  Nonbonded interactions: 69176
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 263 "
            pdb=" CD1 LEU A 267 "
     model   vdw
     1.867 3.460
  nonbonded pdb=" O   ARG S  67 "
            pdb=" OG1 THR S  84 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   LEU R 272 "
            pdb=" OG1 THR R 275 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.286 3.040
  ... (remaining 69171 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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     21.930
  Find NCS groups from input model:        0.090
  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:13.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
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      :  0.006   0.081   8594  Z= 0.374
  Angle     :  0.722  13.488  11745  Z= 0.443
  Chirality :  0.056   0.754   1367
  Planarity :  0.004   0.050   1496
  Dihedral  : 12.812  76.019   2823
  Min Nonbonded Distance : 1.867

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.12 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.49 (0.26), residues: 1133
  helix:  1.67 (0.27), residues: 392
  sheet:  0.31 (0.30), residues: 269
  loop : -0.78 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 332 
 HIS   0.007   0.001   HIS R 165 
 PHE   0.032   0.002   PHE S  68 
 TYR   0.016   0.001   TYR R 163 
 ARG   0.005   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13649 (  442)
  hydrogen bonds       : angle       5.92383 ( 1245)
  SS BOND              : bond        0.00377 (    2)
  SS BOND              : angle       1.00131 (    4)
  covalent geometry    : bond        0.00554 ( 8592)
  covalent geometry    : angle       0.72159 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.7706 (t0) cc_final: 0.7403 (t0)
REVERT: A  307 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7871 (tmm-80)
REVERT: B   88 ASN cc_start: 0.7549 (m110) cc_final: 0.7313 (m110)
REVERT: B  100 VAL cc_start: 0.8389 (p) cc_final: 0.8154 (m)
REVERT: B  175 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7586 (mm-40)
REVERT: B  178 THR cc_start: 0.8654 (m) cc_final: 0.8451 (t)
REVERT: B  283 ARG cc_start: 0.8551 (tpt-90) cc_final: 0.8319 (tpp-160)
REVERT: B  289 TYR cc_start: 0.8305 (m-80) cc_final: 0.7413 (m-80)
REVERT: B  291 ASP cc_start: 0.6365 (t70) cc_final: 0.6161 (t0)
REVERT: S   34 MET cc_start: 0.8099 (mmm) cc_final: 0.7722 (mmm)
REVERT: S  128 MET cc_start: 0.8529 (mtm) cc_final: 0.8255 (mtt)
REVERT: S  218 MET cc_start: 0.7909 (mtp) cc_final: 0.7574 (ttm)
REVERT: R   24 TYR cc_start: 0.7973 (m-10) cc_final: 0.7705 (m-10)
REVERT: R  230 ILE cc_start: 0.8289 (mm) cc_final: 0.8067 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 208
  average time/residue: 0.9027
  time to fit residues: 203.1229
Evaluate side-chains
  192 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   84 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    0.4980
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 110 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 269 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.124230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.109707 restraints weight = 12658.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.91
r_work: 0.3366 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8594  Z= 0.156
  Angle     :  0.560   6.317  11745  Z= 0.296
  Chirality :  0.043   0.144   1367
  Planarity :  0.004   0.054   1496
  Dihedral  :  4.313  23.996   1229
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.33 %
    Favored  : 86.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.65 (0.25), residues: 1133
  helix:  1.91 (0.26), residues: 392
  sheet:  0.27 (0.30), residues: 261
  loop : -0.69 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP R  83 
 HIS   0.005   0.001   HIS R 165 
 PHE   0.022   0.002   PHE S  68 
 TYR   0.019   0.001   TYR S 178 
 ARG   0.008   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  442)
  hydrogen bonds       : angle       4.84191 ( 1245)
  SS BOND              : bond        0.00434 (    2)
  SS BOND              : angle       1.27475 (    4)
  covalent geometry    : bond        0.00355 ( 8592)
  covalent geometry    : angle       0.56001 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  227 ASP cc_start: 0.7886 (t0) cc_final: 0.7560 (t0)
REVERT: B   68 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7937 (tpt90)
REVERT: B   83 ASP cc_start: 0.8232 (t0) cc_final: 0.7837 (t0)
REVERT: B  155 ASN cc_start: 0.8227 (t0) cc_final: 0.7962 (t0)
REVERT: B  158 VAL cc_start: 0.8402 (p) cc_final: 0.8195 (t)
REVERT: B  175 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7978 (mm-40)
REVERT: B  285 LEU cc_start: 0.8265 (tt) cc_final: 0.7970 (tp)
REVERT: B  289 TYR cc_start: 0.8321 (m-80) cc_final: 0.7348 (m-80)
REVERT: B  291 ASP cc_start: 0.6620 (t70) cc_final: 0.6395 (t0)
REVERT: S   34 MET cc_start: 0.8242 (mmm) cc_final: 0.7918 (mmm)
REVERT: S  143 VAL cc_start: 0.8667 (p) cc_final: 0.8351 (m)
REVERT: S  180 MET cc_start: 0.8009 (ttp) cc_final: 0.7776 (ttp)
REVERT: R   66 TYR cc_start: 0.8322 (t80) cc_final: 0.7926 (t80)
REVERT: R   70 LEU cc_start: 0.8734 (tp) cc_final: 0.8526 (tm)
REVERT: R  125 PHE cc_start: 0.8653 (m-80) cc_final: 0.8293 (m-80)
REVERT: R  251 TYR cc_start: 0.8516 (t80) cc_final: 0.7900 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 214
  average time/residue: 0.8770
  time to fit residues: 203.8919
Evaluate side-chains
  207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 197
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue  227 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0060
   chunk 44 optimal weight:    0.3980
   chunk 13 optimal weight:    0.0980
   chunk 91 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0980
   chunk 109 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 105 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.2796

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

Flipped N/Q/H residues before XYZ refinement:
A  43 ASN
A 352 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.126486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.112054 restraints weight = 12814.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3494 rms_B_bonded: 1.91
r_work: 0.3398 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8594  Z= 0.103
  Angle     :  0.509   6.133  11745  Z= 0.269
  Chirality :  0.041   0.136   1367
  Planarity :  0.004   0.050   1496
  Dihedral  :  3.960  24.258   1227
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.32 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.81 (0.25), residues: 1133
  helix:  2.17 (0.26), residues: 391
  sheet:  0.16 (0.30), residues: 266
  loop : -0.61 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R  83 
 HIS   0.006   0.001   HIS R 165 
 PHE   0.023   0.001   PHE R 274 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.009   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  442)
  hydrogen bonds       : angle       4.51934 ( 1245)
  SS BOND              : bond        0.00390 (    2)
  SS BOND              : angle       0.84276 (    4)
  covalent geometry    : bond        0.00224 ( 8592)
  covalent geometry    : angle       0.50861 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 210
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.7854 (t0) cc_final: 0.7586 (t0)
REVERT: B   68 ARG cc_start: 0.8112 (tpt-90) cc_final: 0.7886 (tpt90)
REVERT: B  155 ASN cc_start: 0.8146 (t0) cc_final: 0.7921 (t0)
REVERT: B  175 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7935 (mm-40)
REVERT: B  251 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7600 (mtm-85)
REVERT: B  285 LEU cc_start: 0.8209 (tt) cc_final: 0.7932 (tp)
REVERT: B  291 ASP cc_start: 0.6499 (t70) cc_final: 0.6098 (t70)
REVERT: S   34 MET cc_start: 0.8187 (mmm) cc_final: 0.7823 (mmm)
REVERT: S  143 VAL cc_start: 0.8679 (p) cc_final: 0.8365 (m)
REVERT: S  218 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8063 (ttp)
REVERT: R  124 ARG cc_start: 0.8460 (mtp180) cc_final: 0.8248 (mtp180)
REVERT: R  125 PHE cc_start: 0.8624 (m-80) cc_final: 0.8218 (m-80)
REVERT: R  163 TYR cc_start: 0.8294 (m-10) cc_final: 0.8091 (m-10)
REVERT: R  251 TYR cc_start: 0.8431 (t80) cc_final: 0.7816 (t80)
  outliers start: 24
  outliers final: 11
  residues processed: 216
  average time/residue: 0.9604
  time to fit residues: 223.5405
Evaluate side-chains
  215 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  218 MET
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  183 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 101 optimal weight:    0.6980
   chunk 112 optimal weight:    0.1980
   chunk 15 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.123837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.109454 restraints weight = 12689.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.91
r_work: 0.3355 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8594  Z= 0.146
  Angle     :  0.532   6.088  11745  Z= 0.282
  Chirality :  0.042   0.134   1367
  Planarity :  0.004   0.052   1496
  Dihedral  :  4.019  24.144   1227
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.06 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.70 (0.25), residues: 1133
  helix:  2.09 (0.26), residues: 395
  sheet:  0.01 (0.30), residues: 270
  loop : -0.65 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.006   0.001   HIS R 165 
 PHE   0.022   0.002   PHE S  68 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.009   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03598 (  442)
  hydrogen bonds       : angle       4.55896 ( 1245)
  SS BOND              : bond        0.00444 (    2)
  SS BOND              : angle       0.98004 (    4)
  covalent geometry    : bond        0.00333 ( 8592)
  covalent geometry    : angle       0.53159 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.7834 (t0) cc_final: 0.7574 (t0)
REVERT: A  257 ASN cc_start: 0.8267 (t0) cc_final: 0.8015 (t0)
REVERT: B  150 ARG cc_start: 0.8682 (mmt-90) cc_final: 0.8469 (mmt-90)
REVERT: B  155 ASN cc_start: 0.8184 (t0) cc_final: 0.7971 (t0)
REVERT: B  285 LEU cc_start: 0.8239 (tt) cc_final: 0.8001 (tp)
REVERT: B  289 TYR cc_start: 0.8311 (m-80) cc_final: 0.7278 (m-80)
REVERT: B  291 ASP cc_start: 0.6654 (t70) cc_final: 0.6319 (t70)
REVERT: S   34 MET cc_start: 0.8262 (mmm) cc_final: 0.7913 (mmm)
REVERT: S   83 MET cc_start: 0.6880 (mmm) cc_final: 0.6466 (mmm)
REVERT: S  128 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8286 (mtt)
REVERT: S  143 VAL cc_start: 0.8663 (p) cc_final: 0.8364 (m)
REVERT: S  163 TYR cc_start: 0.8128 (m-80) cc_final: 0.7909 (m-80)
REVERT: R  125 PHE cc_start: 0.8677 (m-80) cc_final: 0.8268 (m-80)
REVERT: R  251 TYR cc_start: 0.8445 (t80) cc_final: 0.7821 (t80)
  outliers start: 23
  outliers final: 12
  residues processed: 204
  average time/residue: 0.8715
  time to fit residues: 192.6202
Evaluate side-chains
  209 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 196
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain R residue   70 LEU
Chi-restraints excluded: chain R residue  183 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
A 322 HIS
B 225 HIS
R 121 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.120865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.106643 restraints weight = 12580.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.88
r_work: 0.3310 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   8594  Z= 0.239
  Angle     :  0.581   6.240  11745  Z= 0.308
  Chirality :  0.044   0.137   1367
  Planarity :  0.004   0.058   1496
  Dihedral  :  4.335  24.569   1227
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.56 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.55 (0.25), residues: 1133
  helix:  1.84 (0.26), residues: 397
  sheet: -0.11 (0.29), residues: 287
  loop : -0.58 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 209 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.022   0.002   PHE S  68 
 TYR   0.022   0.002   TYR R  76 
 ARG   0.011   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04091 (  442)
  hydrogen bonds       : angle       4.72342 ( 1245)
  SS BOND              : bond        0.00565 (    2)
  SS BOND              : angle       1.15959 (    4)
  covalent geometry    : bond        0.00554 ( 8592)
  covalent geometry    : angle       0.58082 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 209
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.7899 (t0) cc_final: 0.7677 (t0)
REVERT: B  130 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7096 (mm-30)
REVERT: B  175 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7983 (mm-40)
REVERT: B  225 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7943 (m-70)
REVERT: B  291 ASP cc_start: 0.6851 (t70) cc_final: 0.6494 (t70)
REVERT: S   34 MET cc_start: 0.8260 (mmm) cc_final: 0.7960 (mmm)
REVERT: S   83 MET cc_start: 0.7247 (mmm) cc_final: 0.6840 (mmm)
REVERT: S  128 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8336 (mtt)
REVERT: S  143 VAL cc_start: 0.8677 (p) cc_final: 0.8407 (m)
REVERT: S  162 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7694 (tt)
REVERT: S  163 TYR cc_start: 0.8154 (m-80) cc_final: 0.7817 (m-80)
REVERT: R  125 PHE cc_start: 0.8727 (m-80) cc_final: 0.8282 (m-80)
REVERT: R  251 TYR cc_start: 0.8529 (t80) cc_final: 0.7976 (t80)
  outliers start: 32
  outliers final: 17
  residues processed: 220
  average time/residue: 0.9133
  time to fit residues: 217.3338
Evaluate side-chains
  223 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 203
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  300 THR
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue  178 VAL
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 94 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.121744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.107477 restraints weight = 12666.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.90
r_work: 0.3320 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8594  Z= 0.194
  Angle     :  0.573   7.132  11745  Z= 0.302
  Chirality :  0.044   0.151   1367
  Planarity :  0.004   0.058   1496
  Dihedral  :  4.263  24.237   1227
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 19.55 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.58 (0.25), residues: 1133
  helix:  1.87 (0.26), residues: 397
  sheet: -0.10 (0.30), residues: 274
  loop : -0.56 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.008   0.001   HIS B 225 
 PHE   0.017   0.002   PHE S  68 
 TYR   0.023   0.002   TYR R  76 
 ARG   0.011   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03829 (  442)
  hydrogen bonds       : angle       4.64715 ( 1245)
  SS BOND              : bond        0.00410 (    2)
  SS BOND              : angle       1.13510 (    4)
  covalent geometry    : bond        0.00447 ( 8592)
  covalent geometry    : angle       0.57283 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 207
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7673 (mt-10)
REVERT: A  227 ASP cc_start: 0.7897 (t0) cc_final: 0.7675 (t0)
REVERT: A  257 ASN cc_start: 0.8201 (t0) cc_final: 0.7994 (t0)
REVERT: B   59 TYR cc_start: 0.8329 (m-80) cc_final: 0.8045 (m-80)
REVERT: B  175 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7983 (mm-40)
REVERT: B  258 ASP cc_start: 0.7745 (t0) cc_final: 0.7540 (t70)
REVERT: B  285 LEU cc_start: 0.8277 (tt) cc_final: 0.8003 (tp)
REVERT: B  291 ASP cc_start: 0.6860 (t70) cc_final: 0.6490 (t70)
REVERT: S   34 MET cc_start: 0.8228 (mmm) cc_final: 0.7969 (mmm)
REVERT: S   83 MET cc_start: 0.7254 (mmm) cc_final: 0.6906 (mmm)
REVERT: S  128 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8383 (mtt)
REVERT: S  143 VAL cc_start: 0.8696 (p) cc_final: 0.8423 (m)
REVERT: S  163 TYR cc_start: 0.8146 (m-80) cc_final: 0.7896 (m-80)
REVERT: R  125 PHE cc_start: 0.8737 (m-80) cc_final: 0.8289 (m-80)
REVERT: R  251 TYR cc_start: 0.8484 (t80) cc_final: 0.7875 (t80)
  outliers start: 33
  outliers final: 16
  residues processed: 218
  average time/residue: 0.8872
  time to fit residues: 209.7283
Evaluate side-chains
  216 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue  245 LEU
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 106 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 85 optimal weight:    0.3980
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
B 176 GLN
B 225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.122951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.108644 restraints weight = 12801.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.93
r_work: 0.3337 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8594  Z= 0.145
  Angle     :  0.556   7.003  11745  Z= 0.291
  Chirality :  0.042   0.138   1367
  Planarity :  0.004   0.056   1496
  Dihedral  :  4.096  24.184   1227
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.79 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.72 (0.25), residues: 1133
  helix:  2.01 (0.26), residues: 396
  sheet: -0.01 (0.30), residues: 265
  loop : -0.51 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 165 
 PHE   0.018   0.001   PHE A 328 
 TYR   0.025   0.002   TYR R  76 
 ARG   0.010   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  442)
  hydrogen bonds       : angle       4.50977 ( 1245)
  SS BOND              : bond        0.00600 (    2)
  SS BOND              : angle       1.00246 (    4)
  covalent geometry    : bond        0.00330 ( 8592)
  covalent geometry    : angle       0.55560 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 193
  time to evaluate  : 1.281 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7652 (mt-10)
REVERT: A  227 ASP cc_start: 0.7886 (t0) cc_final: 0.7673 (t0)
REVERT: B   59 TYR cc_start: 0.8326 (m-80) cc_final: 0.8020 (m-80)
REVERT: B  175 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7992 (mm-40)
REVERT: B  215 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7719 (tt0)
REVERT: B  285 LEU cc_start: 0.8223 (tt) cc_final: 0.7941 (tp)
REVERT: B  291 ASP cc_start: 0.6808 (t70) cc_final: 0.6418 (t70)
REVERT: S   34 MET cc_start: 0.8215 (mmm) cc_final: 0.7948 (mmm)
REVERT: S   83 MET cc_start: 0.7202 (mmm) cc_final: 0.6887 (mmm)
REVERT: S  128 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8360 (mtt)
REVERT: S  143 VAL cc_start: 0.8715 (p) cc_final: 0.8442 (m)
REVERT: S  163 TYR cc_start: 0.8114 (m-80) cc_final: 0.7847 (m-80)
REVERT: R  125 PHE cc_start: 0.8719 (m-80) cc_final: 0.8289 (m-80)
REVERT: R  251 TYR cc_start: 0.8457 (t80) cc_final: 0.7908 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 200
  average time/residue: 1.0036
  time to fit residues: 216.6079
Evaluate side-chains
  206 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 188
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  127 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   84 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 74 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 81 optimal weight:    6.9990
   chunk 23 optimal weight:    9.9990
   chunk 88 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 257 ASN
B  88 ASN
B 176 GLN
R  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.120303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.105933 restraints weight = 12745.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.90
r_work: 0.3303 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   8594  Z= 0.254
  Angle     :  0.615   8.537  11745  Z= 0.323
  Chirality :  0.046   0.166   1367
  Planarity :  0.004   0.059   1496
  Dihedral  :  4.363  24.428   1227
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 21.17 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.54 (0.25), residues: 1133
  helix:  1.78 (0.26), residues: 397
  sheet: -0.14 (0.30), residues: 273
  loop : -0.51 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 209 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.024   0.002   PHE A 328 
 TYR   0.025   0.002   TYR R  76 
 ARG   0.013   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04136 (  442)
  hydrogen bonds       : angle       4.75329 ( 1245)
  SS BOND              : bond        0.00620 (    2)
  SS BOND              : angle       1.21617 (    4)
  covalent geometry    : bond        0.00586 ( 8592)
  covalent geometry    : angle       0.61478 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 206
  time to evaluate  : 0.896 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7695 (mt-10)
REVERT: A  227 ASP cc_start: 0.7894 (t0) cc_final: 0.7678 (t0)
REVERT: B   59 TYR cc_start: 0.8413 (m-80) cc_final: 0.8039 (m-80)
REVERT: B  175 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7986 (mm-40)
REVERT: B  215 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7707 (tt0)
REVERT: B  285 LEU cc_start: 0.8296 (tt) cc_final: 0.8024 (tp)
REVERT: B  291 ASP cc_start: 0.6897 (t70) cc_final: 0.6528 (t70)
REVERT: S   34 MET cc_start: 0.8267 (mmm) cc_final: 0.8028 (mmm)
REVERT: S   83 MET cc_start: 0.7334 (mmm) cc_final: 0.7000 (mmm)
REVERT: S  128 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8375 (mtt)
REVERT: S  143 VAL cc_start: 0.8706 (p) cc_final: 0.8443 (m)
REVERT: S  163 TYR cc_start: 0.8129 (m-80) cc_final: 0.7879 (m-80)
REVERT: R  125 PHE cc_start: 0.8744 (m-80) cc_final: 0.8306 (m-80)
REVERT: R  251 TYR cc_start: 0.8503 (t80) cc_final: 0.7937 (t80)
  outliers start: 36
  outliers final: 22
  residues processed: 216
  average time/residue: 1.1116
  time to fit residues: 260.9794
Evaluate side-chains
  228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 203
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   88 ASN
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  116 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  226 THR
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   84 ILE
Chi-restraints excluded: chain R residue  280 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 83 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   chunk 105 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0870
   chunk 84 optimal weight:    0.0060
   overall best weight:    0.3374

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

Flipped N/Q/H residues before XYZ refinement:
B  88 ASN
B 176 GLN
B 220 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.124143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.109966 restraints weight = 12743.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.92
r_work: 0.3358 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8594  Z= 0.115
  Angle     :  0.570   7.954  11745  Z= 0.297
  Chirality :  0.042   0.179   1367
  Planarity :  0.004   0.054   1496
  Dihedral  :  4.057  24.244   1227
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 22.29 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.79 (0.25), residues: 1133
  helix:  2.07 (0.26), residues: 396
  sheet:  0.00 (0.29), residues: 269
  loop : -0.45 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 155 
 PHE   0.025   0.001   PHE A 328 
 TYR   0.028   0.001   TYR R  76 
 ARG   0.011   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03422 (  442)
  hydrogen bonds       : angle       4.51058 ( 1245)
  SS BOND              : bond        0.00727 (    2)
  SS BOND              : angle       1.31033 (    4)
  covalent geometry    : bond        0.00251 ( 8592)
  covalent geometry    : angle       0.56932 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 191
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7653 (mt-10)
REVERT: A  227 ASP cc_start: 0.7872 (t0) cc_final: 0.7662 (t0)
REVERT: B   59 TYR cc_start: 0.8340 (m-80) cc_final: 0.7937 (m-80)
REVERT: B   86 THR cc_start: 0.8008 (p) cc_final: 0.7677 (p)
REVERT: B  215 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7723 (tt0)
REVERT: B  285 LEU cc_start: 0.8216 (tt) cc_final: 0.7951 (tp)
REVERT: B  291 ASP cc_start: 0.6721 (t70) cc_final: 0.6349 (t70)
REVERT: S   34 MET cc_start: 0.8165 (mmm) cc_final: 0.7917 (mmm)
REVERT: S   83 MET cc_start: 0.7197 (mmm) cc_final: 0.6959 (mmm)
REVERT: S  127 VAL cc_start: 0.8420 (t) cc_final: 0.8195 (p)
REVERT: S  128 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8373 (mtt)
REVERT: S  143 VAL cc_start: 0.8732 (p) cc_final: 0.8450 (m)
REVERT: S  163 TYR cc_start: 0.8048 (m-80) cc_final: 0.7811 (m-80)
REVERT: R  125 PHE cc_start: 0.8712 (m-80) cc_final: 0.8281 (m-80)
REVERT: R  251 TYR cc_start: 0.8394 (t80) cc_final: 0.7764 (t80)
  outliers start: 23
  outliers final: 15
  residues processed: 200
  average time/residue: 0.9768
  time to fit residues: 212.5638
Evaluate side-chains
  204 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 GLU
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  119 VAL
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   57 MET
Chi-restraints excluded: chain R residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 112 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 77 optimal weight:    0.4980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.122792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.108522 restraints weight = 12647.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.92
r_work: 0.3338 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8594  Z= 0.157
  Angle     :  0.580   7.805  11745  Z= 0.306
  Chirality :  0.043   0.186   1367
  Planarity :  0.004   0.053   1496
  Dihedral  :  4.099  24.000   1227
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 24.03 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.77 (0.25), residues: 1133
  helix:  2.05 (0.27), residues: 396
  sheet: -0.02 (0.30), residues: 273
  loop : -0.46 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 155 
 PHE   0.015   0.001   PHE A 328 
 TYR   0.028   0.002   TYR R  76 
 ARG   0.012   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03648 (  442)
  hydrogen bonds       : angle       4.54566 ( 1245)
  SS BOND              : bond        0.00563 (    2)
  SS BOND              : angle       1.91847 (    4)
  covalent geometry    : bond        0.00359 ( 8592)
  covalent geometry    : angle       0.57883 (11741)

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 184
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7678 (mt-10)
REVERT: A  227 ASP cc_start: 0.7869 (t0) cc_final: 0.7630 (t0)
REVERT: B   59 TYR cc_start: 0.8391 (m-80) cc_final: 0.7927 (m-80)
REVERT: B  215 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7728 (tt0)
REVERT: B  291 ASP cc_start: 0.6786 (t70) cc_final: 0.6404 (t70)
REVERT: S   34 MET cc_start: 0.8211 (mmm) cc_final: 0.7960 (mmm)
REVERT: S   83 MET cc_start: 0.7247 (mmm) cc_final: 0.6981 (mmm)
REVERT: S  127 VAL cc_start: 0.8426 (t) cc_final: 0.8191 (p)
REVERT: S  128 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8333 (mtt)
REVERT: S  143 VAL cc_start: 0.8707 (p) cc_final: 0.8435 (m)
REVERT: S  163 TYR cc_start: 0.8042 (m-80) cc_final: 0.7835 (m-80)
REVERT: R  125 PHE cc_start: 0.8720 (m-80) cc_final: 0.8258 (m-80)
REVERT: R  251 TYR cc_start: 0.8421 (t80) cc_final: 0.7937 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 189
  average time/residue: 0.8709
  time to fit residues: 179.0867
Evaluate side-chains
  196 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  130 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   85 SER
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  128 MET
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain R residue   28 ILE
Chi-restraints excluded: chain R residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 10 optimal weight:    0.0770
   chunk 96 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0030
   chunk 20 optimal weight:    0.3980
   chunk 12 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 74 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4350

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.110364 restraints weight = 12783.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.92
r_work: 0.3365 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8594  Z= 0.122
  Angle     :  0.561   8.542  11745  Z= 0.295
  Chirality :  0.042   0.215   1367
  Planarity :  0.004   0.052   1496
  Dihedral  :  3.976  23.902   1227
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 24.03 %
    Favored  : 73.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    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:  0.81 (0.25), residues: 1133
  helix:  2.11 (0.26), residues: 398
  sheet: -0.12 (0.30), residues: 274
  loop : -0.38 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS R 155 
 PHE   0.015   0.001   PHE R 172 
 TYR   0.028   0.001   TYR R  76 
 ARG   0.011   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03423 (  442)
  hydrogen bonds       : angle       4.46306 ( 1245)
  SS BOND              : bond        0.00508 (    2)
  SS BOND              : angle       1.54328 (    4)
  covalent geometry    : bond        0.00270 ( 8592)
  covalent geometry    : angle       0.56056 (11741)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7202.08 seconds
wall clock time: 126 minutes 15.52 seconds (7575.52 seconds total)