Starting phenix.real_space_refine
on Fri Jul 25 12:27:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gy7_34371/07_2025/8gy7_34371_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gy7_34371/07_2025/8gy7_34371.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2025/8gy7_34371.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2025/8gy7_34371.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2025/8gy7_34371_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2025/8gy7_34371_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
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: 5
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S      56      5.16       5
     C    4890      2.51       5
     N    1322      2.21       5
     O    1392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7661
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1920
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 6, 'TRANS': 225}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2604
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "G"
      Number of atoms: 411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 411
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "M"
      Number of atoms: 158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 158
          Classifications: {'peptide': 18}
          Link IDs: {'PTRANS': 1, 'TRANS': 16}
    Chain: "P"
      Number of atoms: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 413
          Classifications: {'peptide': 51}
          Incomplete info: {'backbone_only': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "R"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2154
          Classifications: {'peptide': 274}
          Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 261}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "R"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.86, per 1000 atoms: 0.63
  Number of scatterers: 7661
  At special positions: 0
  Unit cell: (76.96, 120.64, 120.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      1     19.99
     S      56     16.00
     O    1392      8.00
     N    1322      7.00
     C    4890      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  21 " - pdb=" SG  CYS R 253 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 245 " - pdb=" SG  CYS R 251 " distance=2.16

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.97
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1822

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 10 sheets defined
      46.3% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.576A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
    Processing helix  chain 'A' and resid 260 through 270
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
    Processing helix  chain 'A' and resid 298 through 318
      removed outlier: 3.544A  pdb=" N   THR A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE A 315 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 9 through 30
    Processing helix  chain 'B' and resid 34 through 41
      removed outlier: 4.114A  pdb=" N   ASN B  41 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'P' and resid 36 through 63
    Processing helix  chain 'R' and resid 27 through 49
      removed outlier: 3.832A  pdb=" N   PHE R  31 " --> pdb=" O   PRO R  27 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL R  49 " --> pdb=" O   VAL R  45 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 57 through 88
    Processing helix  chain 'R' and resid 96 through 134
      removed outlier: 3.533A  pdb=" N   THR R 101 " --> pdb=" O   SER R  97 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   ALA R 102 " --> pdb=" O   PHE R  98 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 137 through 142
    Processing helix  chain 'R' and resid 143 through 168
    Processing helix  chain 'R' and resid 171 through 208
      removed outlier: 3.875A  pdb=" N   PHE R 182 " --> pdb=" O   PHE R 178 " (cutoff:3.500A)
      Proline residue:  R 183  - end of helix
      removed outlier: 3.647A  pdb=" N   HIS R 195 " --> pdb=" O   CYS R 191 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS R 206 " --> pdb=" O   SER R 202 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 231
    Processing helix  chain 'R' and resid 232 through 245
    Processing helix  chain 'R' and resid 248 through 256
    Processing helix  chain 'R' and resid 257 through 272
      removed outlier: 3.658A  pdb=" N   ASN R 268 " --> pdb=" O   LEU R 264 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   ALA R 269 " --> pdb=" O   ILE R 265 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL R 270 " --> pdb=" O   MET R 266 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 277
    Processing helix  chain 'R' and resid 280 through 291
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186
      removed outlier: 7.070A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.642A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.712A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   CYS B 322 " --> pdb=" O   GLY B 335 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68
      removed outlier: 6.695A  pdb=" N   ALA B  78 " --> pdb=" O   TYR B  64 " (cutoff:3.500A)
      removed outlier: 4.264A  pdb=" N   MET B  66 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   VAL B  76 " --> pdb=" O   MET B  66 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   TRP B  68 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   LEU B  74 " --> pdb=" O   TRP B  68 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   LEU B  84 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA B  97 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 110
      removed outlier: 4.410A  pdb=" N   GLY B 121 " --> pdb=" O   ILE B 125 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   ILE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   CYS B 126 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   GLU B 143 " --> pdb=" O   CYS B 126 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE B 128 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN B 130 " --> pdb=" O   ARG B 139 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ARG B 139 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 158
      removed outlier: 3.507A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   GLN B 161 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   THR B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 192 through 197
      removed outlier: 4.137A  pdb=" N   SER B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239
      removed outlier: 6.958A  pdb=" N   ASP B 259 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   GLU B 265 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.743A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'M' and resid 13 through 15

    415 hydrogen bonds defined for protein.
    1203 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: 2.10

  Time building geometry restraints manager: 2.33 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1311
        1.32 -     1.45: 2079
        1.45 -     1.57: 4347
        1.57 -     1.69: 1
        1.69 -     1.81: 83
  Bond restraints: 7821
  Sorted by residual:
  bond pdb=" C   LEU R 210 "
       pdb=" N   PRO R 211 "
    ideal  model  delta    sigma   weight residual
    1.335  1.412 -0.076 1.30e-02 5.92e+03 3.46e+01
  bond pdb=" CA  ARG A 208 "
       pdb=" C   ARG A 208 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 1.29e-02 6.01e+03 1.68e+01
  bond pdb=" CA  SER R  19 "
       pdb=" CB  SER R  19 "
    ideal  model  delta    sigma   weight residual
    1.529  1.474  0.055 1.64e-02 3.72e+03 1.14e+01
  bond pdb=" C   LYS A  27 "
       pdb=" N   GLN A  28 "
    ideal  model  delta    sigma   weight residual
    1.335  1.297  0.038 1.36e-02 5.41e+03 7.92e+00
  bond pdb=" CB  PRO A 288 "
       pdb=" CG  PRO A 288 "
    ideal  model  delta    sigma   weight residual
    1.492  1.630 -0.138 5.00e-02 4.00e+02 7.65e+00
  ... (remaining 7816 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 10258
        1.95 -     3.90: 268
        3.90 -     5.85: 45
        5.85 -     7.80: 10
        7.80 -     9.75: 4
  Bond angle restraints: 10585
  Sorted by residual:
  angle pdb=" CA  PRO A 288 "
        pdb=" N   PRO A 288 "
        pdb=" CD  PRO A 288 "
      ideal   model   delta    sigma   weight residual
     112.00  102.25    9.75 1.40e+00 5.10e-01 4.85e+01
  angle pdb=" C   CYS R 251 "
        pdb=" CA  CYS R 251 "
        pdb=" CB  CYS R 251 "
      ideal   model   delta    sigma   weight residual
     110.92  101.46    9.46 1.59e+00 3.96e-01 3.54e+01
  angle pdb=" N   SER R 108 "
        pdb=" CA  SER R 108 "
        pdb=" C   SER R 108 "
      ideal   model   delta    sigma   weight residual
     111.14  104.89    6.25 1.08e+00 8.57e-01 3.35e+01
  angle pdb=" C   LYS A  27 "
        pdb=" N   GLN A  28 "
        pdb=" CA  GLN A  28 "
      ideal   model   delta    sigma   weight residual
     120.29  114.02    6.27 1.42e+00 4.96e-01 1.95e+01
  angle pdb=" N   ASN R  54 "
        pdb=" CA  ASN R  54 "
        pdb=" C   ASN R  54 "
      ideal   model   delta    sigma   weight residual
     111.36  106.73    4.63 1.09e+00 8.42e-01 1.81e+01
  ... (remaining 10580 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.02: 3954
       15.02 -    30.04: 476
       30.04 -    45.06: 176
       45.06 -    60.08: 42
       60.08 -    75.10: 10
  Dihedral angle restraints: 4658
    sinusoidal: 1844
      harmonic: 2814
  Sorted by residual:
  dihedral pdb=" CA  LYS A 210 "
           pdb=" C   LYS A 210 "
           pdb=" N   TRP A 211 "
           pdb=" CA  TRP A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.21   25.79     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" C   CYS R 251 "
           pdb=" N   CYS R 251 "
           pdb=" CA  CYS R 251 "
           pdb=" CB  CYS R 251 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.95  -12.65     0      2.50e+00 1.60e-01 2.56e+01
  dihedral pdb=" CA  ASP B 252 "
           pdb=" C   ASP B 252 "
           pdb=" N   ALA B 253 "
           pdb=" CA  ALA B 253 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.82   22.18     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 4655 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1013
       0.059 -    0.117: 154
       0.117 -    0.176: 28
       0.176 -    0.235: 5
       0.235 -    0.294: 1
  Chirality restraints: 1201
  Sorted by residual:
  chirality pdb=" CA  CYS R 251 "
            pdb=" N   CYS R 251 "
            pdb=" C   CYS R 251 "
            pdb=" CB  CYS R 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  SER R  19 "
            pdb=" N   SER R  19 "
            pdb=" C   SER R  19 "
            pdb=" CB  SER R  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE R 154 "
            pdb=" N   ILE R 154 "
            pdb=" C   ILE R 154 "
            pdb=" CB  ILE R 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1198 not shown)

  Planarity restraints: 1339
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 287 "   -0.080 5.00e-02 4.00e+02   1.14e-01 2.09e+01
        pdb=" N   PRO A 288 "    0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R  53 "    0.014 2.00e-02 2.50e+03   2.85e-02 8.10e+00
        pdb=" C   LYS R  53 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   LYS R  53 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ASN R  54 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS R 288 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.12e+00
        pdb=" C   LYS R 288 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   LYS R 288 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS R 289 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1336 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 98
        2.58 -     3.16: 6953
        3.16 -     3.74: 12443
        3.74 -     4.32: 16961
        4.32 -     4.90: 28174
  Nonbonded interactions: 64629
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP R 107 "
            pdb="CA    CA R 501 "
     model   vdw
     2.006 2.510
  nonbonded pdb=" O   ASP B 263 "
            pdb=" OD1 ASP B 263 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG  SER B 284 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   GLU M   5 "
            pdb="CA    CA R 501 "
     model   vdw
     2.262 2.510
  ... (remaining 64624 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:             0.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.500
  Find NCS groups from input model:        0.070
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.138   7823  Z= 0.256
  Angle     :  0.845  28.452  10589  Z= 0.481
  Chirality :  0.047   0.294   1201
  Planarity :  0.006   0.114   1339
  Dihedral  : 15.855  75.099   2830
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 25.42 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.27 (0.27), residues: 954
  helix:  1.45 (0.25), residues: 419
  sheet: -0.08 (0.42), residues: 157
  loop : -1.15 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 248 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.026   0.002   PHE R 157 
 TYR   0.013   0.001   TYR A 230 
 ARG   0.012   0.001   ARG A 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15566 (  415)
  hydrogen bonds       : angle       6.60514 ( 1203)
  SS BOND              : bond        0.08931 (    2)
  SS BOND              : angle      18.84994 (    4)
  covalent geometry    : bond        0.00445 ( 7821)
  covalent geometry    : angle       0.76108 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 261
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8337 (mtpm) cc_final: 0.7870 (mtpm)
REVERT: A  239 ASP cc_start: 0.7896 (m-30) cc_final: 0.7570 (t0)
REVERT: A  337 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7432 (mt-10)
REVERT: B   57 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6743 (mtt90)
REVERT: B   64 TYR cc_start: 0.8217 (m-80) cc_final: 0.7914 (m-80)
REVERT: B   66 MET cc_start: 0.7912 (ptm) cc_final: 0.7629 (ptm)
REVERT: B  116 TYR cc_start: 0.8295 (m-80) cc_final: 0.7675 (m-80)
REVERT: B  178 THR cc_start: 0.8576 (p) cc_final: 0.8213 (t)
REVERT: B  256 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7477 (mtt90)
REVERT: B  268 THR cc_start: 0.8735 (m) cc_final: 0.8490 (p)
REVERT: B  316 HIS cc_start: 0.7748 (m-70) cc_final: 0.7475 (m-70)
REVERT: B  339 SER cc_start: 0.8479 (m) cc_final: 0.8278 (t)
REVERT: B  345 ASN cc_start: 0.7686 (t0) cc_final: 0.7170 (p0)
REVERT: M    4 MET cc_start: 0.7738 (mmt) cc_final: 0.7446 (tpt)
REVERT: R   40 LEU cc_start: 0.7737 (mt) cc_final: 0.7536 (mt)
REVERT: R   77 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6475 (tppp)
REVERT: R  143 THR cc_start: 0.8480 (t) cc_final: 0.8104 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 265
  average time/residue: 0.2652
  time to fit residues: 87.6460
Evaluate side-chains
  262 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 257
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   19 SER
Chi-restraints excluded: chain R residue   77 LYS
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  166 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 GLN
A 324 HIS
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
R  54 ASN
R 214 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.126345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.110692 restraints weight = 11636.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.18
r_work: 0.3255 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7823  Z= 0.184
  Angle     :  0.655   8.245  10589  Z= 0.344
  Chirality :  0.044   0.177   1201
  Planarity :  0.005   0.061   1339
  Dihedral  :  5.522  58.985   1062
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.74 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.50 (0.27), residues: 954
  helix:  1.53 (0.24), residues: 426
  sheet: -0.42 (0.39), residues: 173
  loop : -0.68 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 216 
 HIS   0.013   0.002   HIS B 230 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.019   0.002   TYR A 230 
 ARG   0.007   0.001   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04878 (  415)
  hydrogen bonds       : angle       5.18258 ( 1203)
  SS BOND              : bond        0.00386 (    2)
  SS BOND              : angle       1.71790 (    4)
  covalent geometry    : bond        0.00396 ( 7821)
  covalent geometry    : angle       0.65458 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 265
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7692 (t) cc_final: 0.7442 (p)
REVERT: A  230 TYR cc_start: 0.8688 (m-10) cc_final: 0.8398 (m-10)
REVERT: A  239 ASP cc_start: 0.8257 (m-30) cc_final: 0.7943 (t0)
REVERT: A  267 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8099 (ttpt)
REVERT: A  310 ASP cc_start: 0.7549 (m-30) cc_final: 0.7153 (m-30)
REVERT: A  337 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7870 (mt-10)
REVERT: A  347 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7693 (ttm-80)
REVERT: B   27 ARG cc_start: 0.8147 (mtm180) cc_final: 0.7941 (mtm180)
REVERT: B   37 GLN cc_start: 0.8431 (pm20) cc_final: 0.7974 (pm20)
REVERT: B   47 ARG cc_start: 0.7774 (ptt-90) cc_final: 0.7353 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7444 (mtt90)
REVERT: B   64 TYR cc_start: 0.8327 (m-80) cc_final: 0.7883 (m-80)
REVERT: B   80 GLN cc_start: 0.7319 (mt0) cc_final: 0.6591 (mt0)
REVERT: B  115 ASN cc_start: 0.8399 (m110) cc_final: 0.7940 (m-40)
REVERT: B  119 CYS cc_start: 0.8475 (p) cc_final: 0.8192 (p)
REVERT: B  142 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7540 (tpp80)
REVERT: B  235 ASN cc_start: 0.8200 (m-40) cc_final: 0.7942 (m110)
REVERT: B  255 CYS cc_start: 0.8116 (t) cc_final: 0.7681 (p)
REVERT: B  279 THR cc_start: 0.8458 (m) cc_final: 0.8254 (p)
REVERT: B  309 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7723 (mtm-85)
REVERT: B  316 HIS cc_start: 0.7796 (m-70) cc_final: 0.7514 (m-70)
REVERT: B  338 ASP cc_start: 0.8053 (p0) cc_final: 0.7648 (p0)
REVERT: B  339 SER cc_start: 0.8432 (m) cc_final: 0.8021 (t)
REVERT: B  345 ASN cc_start: 0.7662 (t0) cc_final: 0.6952 (p0)
REVERT: M    4 MET cc_start: 0.7585 (mmt) cc_final: 0.7367 (tpp)
REVERT: R  271 ILE cc_start: 0.8580 (tt) cc_final: 0.8370 (tt)
  outliers start: 28
  outliers final: 16
  residues processed: 278
  average time/residue: 0.2410
  time to fit residues: 84.6560
Evaluate side-chains
  277 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 259
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  204 THR
Chi-restraints excluded: chain R residue  214 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0170
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0570
   chunk 15 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.4336

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 195 ASN
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 GLN
B 225 GLN
B 242 ASN
R 214 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.127557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.111791 restraints weight = 11775.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.22
r_work: 0.3272 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7823  Z= 0.140
  Angle     :  0.594   7.804  10589  Z= 0.314
  Chirality :  0.042   0.156   1201
  Planarity :  0.004   0.057   1339
  Dihedral  :  5.124  58.667   1055
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 21.94 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.71 (0.28), residues: 954
  helix:  1.76 (0.25), residues: 421
  sheet: -0.53 (0.39), residues: 176
  loop : -0.47 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 174 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.012   0.001   TYR A 230 
 ARG   0.007   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04349 (  415)
  hydrogen bonds       : angle       4.96706 ( 1203)
  SS BOND              : bond        0.00514 (    2)
  SS BOND              : angle       1.83570 (    4)
  covalent geometry    : bond        0.00301 ( 7821)
  covalent geometry    : angle       0.59350 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 255
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7626 (t) cc_final: 0.7383 (p)
REVERT: A  230 TYR cc_start: 0.8685 (m-10) cc_final: 0.8371 (m-10)
REVERT: A  239 ASP cc_start: 0.8321 (m-30) cc_final: 0.8017 (t0)
REVERT: A  267 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8118 (ttpt)
REVERT: A  274 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8597 (mptt)
REVERT: A  340 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8100 (tpt170)
REVERT: A  347 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7523 (ttm-80)
REVERT: A  351 GLN cc_start: 0.8504 (mt0) cc_final: 0.8191 (mt0)
REVERT: B   47 ARG cc_start: 0.7764 (ptt-90) cc_final: 0.7381 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7407 (mtt90)
REVERT: B   64 TYR cc_start: 0.8336 (m-80) cc_final: 0.7995 (m-80)
REVERT: B   67 HIS cc_start: 0.8597 (t70) cc_final: 0.8390 (t70)
REVERT: B  115 ASN cc_start: 0.8446 (m110) cc_final: 0.7982 (m-40)
REVERT: B  116 TYR cc_start: 0.8475 (m-80) cc_final: 0.7806 (m-80)
REVERT: B  117 VAL cc_start: 0.8819 (p) cc_final: 0.8549 (t)
REVERT: B  142 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7466 (tpp80)
REVERT: B  159 ASP cc_start: 0.8023 (m-30) cc_final: 0.7463 (m-30)
REVERT: B  176 ILE cc_start: 0.8547 (mm) cc_final: 0.7555 (mm)
REVERT: B  255 CYS cc_start: 0.8193 (t) cc_final: 0.7683 (p)
REVERT: B  256 ARG cc_start: 0.8430 (mtt-85) cc_final: 0.7677 (mtt180)
REVERT: B  259 ASP cc_start: 0.7985 (t0) cc_final: 0.7735 (t0)
REVERT: B  279 THR cc_start: 0.8423 (m) cc_final: 0.8200 (p)
REVERT: B  280 SER cc_start: 0.8641 (t) cc_final: 0.8060 (p)
REVERT: B  309 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7664 (mtm-85)
REVERT: B  316 HIS cc_start: 0.7774 (m-70) cc_final: 0.7462 (m-70)
REVERT: B  328 ASP cc_start: 0.8119 (p0) cc_final: 0.7911 (p0)
REVERT: B  336 SER cc_start: 0.8379 (t) cc_final: 0.8066 (t)
REVERT: B  338 ASP cc_start: 0.7979 (p0) cc_final: 0.7593 (p0)
REVERT: B  339 SER cc_start: 0.8426 (m) cc_final: 0.7941 (t)
REVERT: R   53 LYS cc_start: 0.8589 (tppt) cc_final: 0.8132 (ttpt)
REVERT: R  195 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7384 (t70)
  outliers start: 33
  outliers final: 17
  residues processed: 269
  average time/residue: 0.2782
  time to fit residues: 95.6435
Evaluate side-chains
  273 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 252
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  327 ASP
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   68 ILE
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0270
   chunk 69 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 244 ASN
B 318 ASN
G  24 ASN
R 214 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.126749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111647 restraints weight = 11861.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.16
r_work: 0.3284 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7823  Z= 0.145
  Angle     :  0.580   7.335  10589  Z= 0.304
  Chirality :  0.042   0.167   1201
  Planarity :  0.004   0.052   1339
  Dihedral  :  4.685  22.042   1053
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 21.70 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.71 (0.27), residues: 954
  helix:  1.73 (0.24), residues: 426
  sheet: -0.58 (0.39), residues: 176
  loop : -0.45 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 174 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.018   0.001   PHE A 189 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.004   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04168 (  415)
  hydrogen bonds       : angle       4.84463 ( 1203)
  SS BOND              : bond        0.00344 (    2)
  SS BOND              : angle       2.40248 (    4)
  covalent geometry    : bond        0.00309 ( 7821)
  covalent geometry    : angle       0.57872 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 252
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7597 (t) cc_final: 0.7361 (p)
REVERT: A   19 ILE cc_start: 0.8352 (tp) cc_final: 0.7857 (tp)
REVERT: A  230 TYR cc_start: 0.8673 (m-10) cc_final: 0.8398 (m-10)
REVERT: A  239 ASP cc_start: 0.8203 (m-30) cc_final: 0.7877 (t0)
REVERT: A  267 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8057 (ttpt)
REVERT: A  274 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8647 (mptt)
REVERT: A  340 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.8109 (tpt170)
REVERT: A  347 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7745 (ttm-80)
REVERT: B   37 GLN cc_start: 0.8575 (pm20) cc_final: 0.8371 (pm20)
REVERT: B   47 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7373 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7754 (mtt90) cc_final: 0.7391 (mtt90)
REVERT: B   64 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7972 (m-80)
REVERT: B   67 HIS cc_start: 0.8583 (t70) cc_final: 0.8383 (t70)
REVERT: B  115 ASN cc_start: 0.8486 (m110) cc_final: 0.8005 (m-40)
REVERT: B  116 TYR cc_start: 0.8447 (m-80) cc_final: 0.7804 (m-80)
REVERT: B  117 VAL cc_start: 0.8790 (p) cc_final: 0.8526 (t)
REVERT: B  142 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7429 (tpp80)
REVERT: B  159 ASP cc_start: 0.8034 (m-30) cc_final: 0.7452 (m-30)
REVERT: B  176 ILE cc_start: 0.8599 (mm) cc_final: 0.7639 (mm)
REVERT: B  235 ASN cc_start: 0.8094 (m-40) cc_final: 0.7840 (m110)
REVERT: B  239 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7813 (m-80)
REVERT: B  244 ASN cc_start: 0.8310 (m-40) cc_final: 0.7937 (t0)
REVERT: B  255 CYS cc_start: 0.8113 (t) cc_final: 0.7734 (p)
REVERT: B  263 ASP cc_start: 0.8052 (t0) cc_final: 0.7580 (t0)
REVERT: B  279 THR cc_start: 0.8440 (m) cc_final: 0.8213 (p)
REVERT: B  309 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7735 (mtm-85)
REVERT: B  328 ASP cc_start: 0.8100 (p0) cc_final: 0.7888 (p0)
REVERT: B  339 SER cc_start: 0.8370 (m) cc_final: 0.7935 (t)
REVERT: R   53 LYS cc_start: 0.8591 (tppt) cc_final: 0.8126 (ttpt)
REVERT: R  195 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7283 (t70)
REVERT: R  242 MET cc_start: 0.8382 (tmm) cc_final: 0.8064 (ttp)
REVERT: R  266 MET cc_start: 0.8131 (mmm) cc_final: 0.7554 (mmm)
  outliers start: 39
  outliers final: 24
  residues processed: 270
  average time/residue: 0.2503
  time to fit residues: 85.2611
Evaluate side-chains
  282 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 252
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain P residue   24 ILE
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   47 LEU
Chi-restraints excluded: chain R residue   68 ILE
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Chi-restraints excluded: chain R residue  214 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 73 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 351 GLN
B 225 GLN
R 214 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.126283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.111132 restraints weight = 11794.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.17
r_work: 0.3267 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7823  Z= 0.172
  Angle     :  0.592   7.652  10589  Z= 0.311
  Chirality :  0.043   0.178   1201
  Planarity :  0.004   0.048   1339
  Dihedral  :  4.699  22.564   1053
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.54 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.68 (0.27), residues: 954
  helix:  1.69 (0.24), residues: 426
  sheet: -0.54 (0.39), residues: 176
  loop : -0.46 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 104 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.017   0.002   PHE B 246 
 TYR   0.010   0.001   TYR B 150 
 ARG   0.004   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  415)
  hydrogen bonds       : angle       4.82525 ( 1203)
  SS BOND              : bond        0.00433 (    2)
  SS BOND              : angle       1.87300 (    4)
  covalent geometry    : bond        0.00368 ( 7821)
  covalent geometry    : angle       0.59059 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 253
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7609 (t) cc_final: 0.7370 (p)
REVERT: A   19 ILE cc_start: 0.8355 (tp) cc_final: 0.7859 (tp)
REVERT: A  230 TYR cc_start: 0.8699 (m-10) cc_final: 0.8486 (m-10)
REVERT: A  234 GLN cc_start: 0.8761 (tp40) cc_final: 0.8531 (tp-100)
REVERT: A  239 ASP cc_start: 0.8219 (m-30) cc_final: 0.7930 (t0)
REVERT: A  267 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8080 (ttpt)
REVERT: A  274 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8683 (mptt)
REVERT: A  313 LEU cc_start: 0.8646 (mm) cc_final: 0.8258 (mt)
REVERT: A  321 ASP cc_start: 0.8002 (t0) cc_final: 0.7623 (t0)
REVERT: A  323 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7571 (mtm180)
REVERT: A  340 ARG cc_start: 0.8528 (tpp-160) cc_final: 0.8138 (tpt170)
REVERT: A  347 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7683 (ttm-80)
REVERT: B   27 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7624 (mtt180)
REVERT: B   47 ARG cc_start: 0.7817 (ptt-90) cc_final: 0.7455 (ptt-90)
REVERT: B   55 THR cc_start: 0.7887 (m) cc_final: 0.6196 (p)
REVERT: B   57 ARG cc_start: 0.7790 (mtt90) cc_final: 0.6821 (mtt90)
REVERT: B   64 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7967 (m-80)
REVERT: B  104 TRP cc_start: 0.8628 (m100) cc_final: 0.8006 (m100)
REVERT: B  115 ASN cc_start: 0.8507 (m110) cc_final: 0.8012 (m-40)
REVERT: B  117 VAL cc_start: 0.8793 (p) cc_final: 0.8525 (t)
REVERT: B  142 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7479 (tpp80)
REVERT: B  176 ILE cc_start: 0.8602 (mm) cc_final: 0.7662 (mm)
REVERT: B  244 ASN cc_start: 0.8231 (m-40) cc_final: 0.7839 (t0)
REVERT: B  255 CYS cc_start: 0.8095 (t) cc_final: 0.7698 (p)
REVERT: B  256 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.7667 (mtt180)
REVERT: B  263 ASP cc_start: 0.7930 (t0) cc_final: 0.7654 (t0)
REVERT: B  279 THR cc_start: 0.8424 (m) cc_final: 0.8205 (p)
REVERT: B  309 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7731 (mtm-85)
REVERT: B  328 ASP cc_start: 0.8115 (p0) cc_final: 0.7902 (p0)
REVERT: B  338 ASP cc_start: 0.7953 (p0) cc_final: 0.7613 (p0)
REVERT: B  339 SER cc_start: 0.8347 (m) cc_final: 0.7877 (t)
REVERT: B  345 ASN cc_start: 0.7770 (t0) cc_final: 0.7150 (p0)
REVERT: R   53 LYS cc_start: 0.8596 (tppt) cc_final: 0.8130 (ttpt)
REVERT: R  195 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7305 (t70)
REVERT: R  242 MET cc_start: 0.8375 (tmm) cc_final: 0.8020 (ttp)
REVERT: R  266 MET cc_start: 0.8143 (mmm) cc_final: 0.7529 (mmm)
  outliers start: 37
  outliers final: 24
  residues processed: 269
  average time/residue: 0.2540
  time to fit residues: 86.5803
Evaluate side-chains
  274 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 245
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  327 ASP
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  227 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 76 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 79 optimal weight:    0.0370
   chunk 91 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0970
   chunk 43 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.3856

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
B 318 ASN
R 214 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.111985 restraints weight = 11704.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.14
r_work: 0.3290 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7823  Z= 0.127
  Angle     :  0.563   7.951  10589  Z= 0.295
  Chirality :  0.041   0.170   1201
  Planarity :  0.004   0.046   1339
  Dihedral  :  4.598  21.035   1053
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 23.02 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.27), residues: 954
  helix:  1.80 (0.24), residues: 426
  sheet: -0.59 (0.38), residues: 176
  loop : -0.51 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 174 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.018   0.001   PHE B 246 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.004   0.000   ARG R  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  415)
  hydrogen bonds       : angle       4.73690 ( 1203)
  SS BOND              : bond        0.00549 (    2)
  SS BOND              : angle       1.55228 (    4)
  covalent geometry    : bond        0.00270 ( 7821)
  covalent geometry    : angle       0.56242 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 253
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A   13 VAL cc_start: 0.7601 (t) cc_final: 0.7351 (p)
REVERT: A   19 ILE cc_start: 0.8343 (tp) cc_final: 0.7851 (tp)
REVERT: A  210 LYS cc_start: 0.8256 (mttm) cc_final: 0.8021 (mttm)
REVERT: A  230 TYR cc_start: 0.8710 (m-10) cc_final: 0.8415 (m-10)
REVERT: A  239 ASP cc_start: 0.8153 (m-30) cc_final: 0.7855 (t0)
REVERT: A  241 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8493 (ttmm)
REVERT: A  260 LYS cc_start: 0.8783 (mtmp) cc_final: 0.8038 (mtmm)
REVERT: A  267 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8084 (ttpt)
REVERT: A  274 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8689 (mptt)
REVERT: A  313 LEU cc_start: 0.8624 (mm) cc_final: 0.8226 (mt)
REVERT: A  321 ASP cc_start: 0.8008 (t0) cc_final: 0.7736 (t0)
REVERT: A  340 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.8127 (tpt170)
REVERT: A  347 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7483 (ttm-80)
REVERT: A  351 GLN cc_start: 0.8561 (mt0) cc_final: 0.8290 (mt0)
REVERT: B   27 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7590 (mtt180)
REVERT: B   37 GLN cc_start: 0.8512 (pm20) cc_final: 0.8287 (pm20)
REVERT: B   47 ARG cc_start: 0.7847 (ptt-90) cc_final: 0.7641 (ptt-90)
REVERT: B   64 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7980 (m-80)
REVERT: B   90 TYR cc_start: 0.7442 (m-10) cc_final: 0.7199 (m-80)
REVERT: B  104 TRP cc_start: 0.8606 (m100) cc_final: 0.7989 (m100)
REVERT: B  115 ASN cc_start: 0.8531 (m110) cc_final: 0.8047 (m110)
REVERT: B  116 TYR cc_start: 0.8455 (m-80) cc_final: 0.7752 (m-80)
REVERT: B  117 VAL cc_start: 0.8762 (p) cc_final: 0.8525 (t)
REVERT: B  142 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7292 (tpp80)
REVERT: B  175 ASP cc_start: 0.7193 (m-30) cc_final: 0.6797 (m-30)
REVERT: B  222 MET cc_start: 0.7409 (mmm) cc_final: 0.7150 (mmm)
REVERT: B  225 GLN cc_start: 0.8241 (mt0) cc_final: 0.7758 (mt0)
REVERT: B  239 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7848 (m-80)
REVERT: B  244 ASN cc_start: 0.8173 (m-40) cc_final: 0.7902 (t0)
REVERT: B  255 CYS cc_start: 0.8120 (t) cc_final: 0.7750 (p)
REVERT: B  256 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.7945 (mtt90)
REVERT: B  263 ASP cc_start: 0.7817 (t0) cc_final: 0.7421 (t70)
REVERT: B  278 ILE cc_start: 0.8089 (mp) cc_final: 0.7888 (mt)
REVERT: B  279 THR cc_start: 0.8382 (m) cc_final: 0.8164 (p)
REVERT: B  309 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.7806 (mtm-85)
REVERT: B  328 ASP cc_start: 0.8068 (p0) cc_final: 0.7853 (p0)
REVERT: B  338 ASP cc_start: 0.7924 (p0) cc_final: 0.7635 (p0)
REVERT: R   30 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7232 (tp)
REVERT: R   53 LYS cc_start: 0.8509 (tppt) cc_final: 0.8037 (ttpt)
REVERT: R  195 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7236 (t70)
REVERT: R  245 CYS cc_start: 0.7723 (p) cc_final: 0.7502 (p)
REVERT: R  266 MET cc_start: 0.8100 (mmm) cc_final: 0.7507 (mmm)
  outliers start: 40
  outliers final: 25
  residues processed: 270
  average time/residue: 0.2539
  time to fit residues: 86.1602
Evaluate side-chains
  278 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 246
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  274 LYS
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   30 ILE
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  227 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 59 optimal weight:    0.0670
   chunk 21 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0470
   chunk 46 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
B  67 HIS
B 235 ASN
B 318 ASN
R 214 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.127849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.112824 restraints weight = 11735.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.18
r_work: 0.3291 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7823  Z= 0.126
  Angle     :  0.568   8.138  10589  Z= 0.298
  Chirality :  0.041   0.182   1201
  Planarity :  0.004   0.043   1339
  Dihedral  :  4.533  21.180   1053
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.38 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.74 (0.27), residues: 954
  helix:  1.83 (0.24), residues: 426
  sheet: -0.60 (0.38), residues: 176
  loop : -0.52 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.008   0.001   HIS A 329 
 PHE   0.019   0.001   PHE B 246 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.007   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03947 (  415)
  hydrogen bonds       : angle       4.68717 ( 1203)
  SS BOND              : bond        0.00466 (    2)
  SS BOND              : angle       1.40183 (    4)
  covalent geometry    : bond        0.00271 ( 7821)
  covalent geometry    : angle       0.56746 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 252
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A   13 VAL cc_start: 0.7555 (t) cc_final: 0.7270 (p)
REVERT: A   19 ILE cc_start: 0.8353 (tp) cc_final: 0.7864 (tp)
REVERT: A  210 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8092 (mttm)
REVERT: A  230 TYR cc_start: 0.8708 (m-10) cc_final: 0.8420 (m-10)
REVERT: A  239 ASP cc_start: 0.8143 (m-30) cc_final: 0.7832 (t0)
REVERT: A  260 LYS cc_start: 0.8739 (mtmp) cc_final: 0.7923 (mtmm)
REVERT: A  267 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8040 (ttpt)
REVERT: A  313 LEU cc_start: 0.8590 (mm) cc_final: 0.8175 (mt)
REVERT: A  321 ASP cc_start: 0.8029 (t0) cc_final: 0.7643 (t0)
REVERT: A  323 ARG cc_start: 0.8084 (mtm180) cc_final: 0.7572 (mtm180)
REVERT: A  340 ARG cc_start: 0.8508 (tpp-160) cc_final: 0.8109 (tpt170)
REVERT: A  347 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7487 (ttm-80)
REVERT: A  351 GLN cc_start: 0.8589 (mt0) cc_final: 0.8351 (mt0)
REVERT: B   27 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7569 (mtt180)
REVERT: B   37 GLN cc_start: 0.8494 (pm20) cc_final: 0.8238 (pm20)
REVERT: B   64 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7978 (m-80)
REVERT: B  104 TRP cc_start: 0.8609 (m100) cc_final: 0.7973 (m100)
REVERT: B  115 ASN cc_start: 0.8548 (m110) cc_final: 0.8065 (m110)
REVERT: B  116 TYR cc_start: 0.8446 (m-80) cc_final: 0.7764 (m-80)
REVERT: B  117 VAL cc_start: 0.8745 (p) cc_final: 0.8519 (t)
REVERT: B  142 ARG cc_start: 0.7966 (tpp80) cc_final: 0.7295 (tpp80)
REVERT: B  175 ASP cc_start: 0.7194 (m-30) cc_final: 0.6768 (m-30)
REVERT: B  222 MET cc_start: 0.7431 (mmm) cc_final: 0.7155 (mmm)
REVERT: B  224 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7286 (ttm110)
REVERT: B  225 GLN cc_start: 0.8268 (mt0) cc_final: 0.7819 (mt0)
REVERT: B  239 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7858 (m-80)
REVERT: B  244 ASN cc_start: 0.8118 (m-40) cc_final: 0.7789 (t0)
REVERT: B  255 CYS cc_start: 0.8171 (t) cc_final: 0.7778 (p)
REVERT: B  256 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.7752 (ttm110)
REVERT: B  263 ASP cc_start: 0.7789 (t0) cc_final: 0.7402 (t70)
REVERT: B  268 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8409 (t)
REVERT: B  279 THR cc_start: 0.8386 (m) cc_final: 0.8166 (p)
REVERT: B  309 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7829 (mtm-85)
REVERT: B  328 ASP cc_start: 0.8071 (p0) cc_final: 0.7866 (p0)
REVERT: B  338 ASP cc_start: 0.7835 (p0) cc_final: 0.7591 (p0)
REVERT: R   30 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7190 (tp)
REVERT: R   87 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7754 (ttp-170)
REVERT: R  195 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7220 (t70)
REVERT: R  215 MET cc_start: 0.7701 (tpp) cc_final: 0.7466 (tpp)
REVERT: R  245 CYS cc_start: 0.7757 (p) cc_final: 0.7529 (p)
  outliers start: 41
  outliers final: 29
  residues processed: 270
  average time/residue: 0.2534
  time to fit residues: 86.2620
Evaluate side-chains
  285 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 249
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   49 GLN
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain B residue  330 MET
Chi-restraints excluded: chain P residue   52 LEU
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   30 ILE
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  227 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 82 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 235 ASN
B 318 ASN
R 214 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.126747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.111423 restraints weight = 11846.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.18
r_work: 0.3277 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7823  Z= 0.165
  Angle     :  0.591   8.602  10589  Z= 0.309
  Chirality :  0.042   0.189   1201
  Planarity :  0.004   0.042   1339
  Dihedral  :  4.565  22.210   1053
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.98 %
    Favored  : 71.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.27), residues: 954
  helix:  1.79 (0.24), residues: 426
  sheet: -0.62 (0.38), residues: 176
  loop : -0.54 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.019   0.002   PHE B 246 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.008   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04030 (  415)
  hydrogen bonds       : angle       4.71406 ( 1203)
  SS BOND              : bond        0.00483 (    2)
  SS BOND              : angle       1.35497 (    4)
  covalent geometry    : bond        0.00356 ( 7821)
  covalent geometry    : angle       0.59003 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 252
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7610 (t) cc_final: 0.7345 (p)
REVERT: A   19 ILE cc_start: 0.8367 (tp) cc_final: 0.7888 (tp)
REVERT: A  210 LYS cc_start: 0.8295 (mmtm) cc_final: 0.8056 (mmtm)
REVERT: A  230 TYR cc_start: 0.8769 (m-10) cc_final: 0.8436 (m-10)
REVERT: A  232 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8091 (mtp85)
REVERT: A  239 ASP cc_start: 0.8206 (m-30) cc_final: 0.7907 (t0)
REVERT: A  260 LYS cc_start: 0.8723 (mtmp) cc_final: 0.7902 (mtmm)
REVERT: A  267 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8065 (ttpt)
REVERT: A  274 LYS cc_start: 0.8966 (mptt) cc_final: 0.8701 (mptt)
REVERT: A  313 LEU cc_start: 0.8607 (mm) cc_final: 0.8204 (mt)
REVERT: A  321 ASP cc_start: 0.8058 (t0) cc_final: 0.7675 (t0)
REVERT: A  323 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7590 (mtm180)
REVERT: A  340 ARG cc_start: 0.8534 (tpp-160) cc_final: 0.8144 (tpt170)
REVERT: A  347 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7641 (ttm-80)
REVERT: B   47 ARG cc_start: 0.7929 (ptt-90) cc_final: 0.7613 (ptt-90)
REVERT: B   49 GLN cc_start: 0.7366 (pt0) cc_final: 0.7131 (pt0)
REVERT: B   64 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7943 (m-80)
REVERT: B   79 SER cc_start: 0.8558 (p) cc_final: 0.8213 (p)
REVERT: B  104 TRP cc_start: 0.8626 (m100) cc_final: 0.7979 (m100)
REVERT: B  115 ASN cc_start: 0.8556 (m110) cc_final: 0.8077 (m110)
REVERT: B  117 VAL cc_start: 0.8773 (p) cc_final: 0.8522 (t)
REVERT: B  142 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7364 (tpp80)
REVERT: B  175 ASP cc_start: 0.7189 (m-30) cc_final: 0.6770 (m-30)
REVERT: B  222 MET cc_start: 0.7402 (mmm) cc_final: 0.7106 (mmm)
REVERT: B  225 GLN cc_start: 0.8283 (mt0) cc_final: 0.7857 (mt0)
REVERT: B  239 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7866 (m-80)
REVERT: B  244 ASN cc_start: 0.8117 (m-40) cc_final: 0.7748 (t0)
REVERT: B  263 ASP cc_start: 0.7751 (t0) cc_final: 0.7365 (t70)
REVERT: B  279 THR cc_start: 0.8382 (m) cc_final: 0.8168 (p)
REVERT: B  309 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8062 (mtm-85)
REVERT: B  338 ASP cc_start: 0.7823 (p0) cc_final: 0.7598 (p0)
REVERT: R   30 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7212 (tp)
REVERT: R   39 VAL cc_start: 0.8219 (t) cc_final: 0.8017 (t)
REVERT: R  195 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7296 (t70)
REVERT: R  215 MET cc_start: 0.7749 (tpp) cc_final: 0.7514 (tpp)
REVERT: R  242 MET cc_start: 0.8235 (ttp) cc_final: 0.7891 (ttp)
REVERT: R  245 CYS cc_start: 0.7704 (p) cc_final: 0.7458 (p)
  outliers start: 41
  outliers final: 29
  residues processed: 270
  average time/residue: 0.2614
  time to fit residues: 89.0434
Evaluate side-chains
  287 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 252
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  180 GLN
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain P residue   24 ILE
Chi-restraints excluded: chain P residue   52 LEU
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   30 ILE
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Chi-restraints excluded: chain R residue  214 ASN
Chi-restraints excluded: chain R residue  227 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 64 optimal weight:    0.3980
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 78 optimal weight:    0.2980
   chunk 52 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 88 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B  93 ASN
B 318 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.111874 restraints weight = 11924.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.21
r_work: 0.3282 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7823  Z= 0.143
  Angle     :  0.595   9.851  10589  Z= 0.311
  Chirality :  0.043   0.240   1201
  Planarity :  0.004   0.042   1339
  Dihedral  :  4.565  21.578   1053
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 25.06 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.71 (0.27), residues: 954
  helix:  1.83 (0.24), residues: 426
  sheet: -0.63 (0.38), residues: 178
  loop : -0.56 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.020   0.001   PHE B 246 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.007   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  415)
  hydrogen bonds       : angle       4.73485 ( 1203)
  SS BOND              : bond        0.00415 (    2)
  SS BOND              : angle       1.19897 (    4)
  covalent geometry    : bond        0.00313 ( 7821)
  covalent geometry    : angle       0.59447 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 248
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7581 (t) cc_final: 0.7324 (p)
REVERT: A   19 ILE cc_start: 0.8365 (tp) cc_final: 0.7884 (tp)
REVERT: A   20 GLU cc_start: 0.7792 (tp30) cc_final: 0.7534 (tp30)
REVERT: A  210 LYS cc_start: 0.8277 (mmtm) cc_final: 0.8031 (mmtm)
REVERT: A  230 TYR cc_start: 0.8776 (m-10) cc_final: 0.8521 (m-10)
REVERT: A  232 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8121 (mtp85)
REVERT: A  239 ASP cc_start: 0.8130 (m-30) cc_final: 0.7822 (t0)
REVERT: A  260 LYS cc_start: 0.8707 (mtmp) cc_final: 0.7871 (mtmm)
REVERT: A  267 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8057 (ttpt)
REVERT: A  274 LYS cc_start: 0.8963 (mptt) cc_final: 0.8691 (mptt)
REVERT: A  313 LEU cc_start: 0.8597 (mm) cc_final: 0.8185 (mt)
REVERT: A  321 ASP cc_start: 0.8041 (t0) cc_final: 0.7661 (t0)
REVERT: A  323 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7579 (mtm180)
REVERT: A  340 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.8137 (tpt170)
REVERT: A  347 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7689 (ttm-80)
REVERT: B   47 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.7593 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7682 (mtt90) cc_final: 0.7297 (mtt90)
REVERT: B   79 SER cc_start: 0.8527 (p) cc_final: 0.8166 (p)
REVERT: B  104 TRP cc_start: 0.8609 (m100) cc_final: 0.7951 (m100)
REVERT: B  115 ASN cc_start: 0.8541 (m110) cc_final: 0.8054 (m110)
REVERT: B  116 TYR cc_start: 0.8453 (m-80) cc_final: 0.7765 (m-80)
REVERT: B  117 VAL cc_start: 0.8767 (p) cc_final: 0.8532 (t)
REVERT: B  142 ARG cc_start: 0.8013 (tpp80) cc_final: 0.7362 (tpp80)
REVERT: B  175 ASP cc_start: 0.7172 (m-30) cc_final: 0.6775 (m-30)
REVERT: B  210 ASP cc_start: 0.7460 (p0) cc_final: 0.7176 (p0)
REVERT: B  222 MET cc_start: 0.7420 (mmm) cc_final: 0.7164 (mmm)
REVERT: B  225 GLN cc_start: 0.8265 (mt0) cc_final: 0.8046 (mt0)
REVERT: B  239 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7865 (m-80)
REVERT: B  244 ASN cc_start: 0.8113 (m-40) cc_final: 0.7744 (t0)
REVERT: B  255 CYS cc_start: 0.8166 (t) cc_final: 0.7717 (p)
REVERT: B  256 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7727 (mtt90)
REVERT: B  263 ASP cc_start: 0.7857 (t0) cc_final: 0.7501 (t70)
REVERT: B  268 THR cc_start: 0.8771 (t) cc_final: 0.8475 (t)
REVERT: B  279 THR cc_start: 0.8376 (m) cc_final: 0.8169 (p)
REVERT: B  309 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.8015 (mtm-85)
REVERT: B  338 ASP cc_start: 0.7834 (p0) cc_final: 0.7582 (p0)
REVERT: R   30 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7186 (tp)
REVERT: R  195 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7223 (t70)
REVERT: R  242 MET cc_start: 0.8246 (ttp) cc_final: 0.7897 (ttp)
REVERT: R  245 CYS cc_start: 0.7706 (p) cc_final: 0.7453 (p)
  outliers start: 38
  outliers final: 27
  residues processed: 266
  average time/residue: 0.2691
  time to fit residues: 90.1704
Evaluate side-chains
  282 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 250
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  180 GLN
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain P residue   24 ILE
Chi-restraints excluded: chain P residue   52 LEU
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   30 ILE
Chi-restraints excluded: chain R residue   75 LEU
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Chi-restraints excluded: chain R residue  227 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  49 GLN
B 318 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.126009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.110686 restraints weight = 11854.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.19
r_work: 0.3265 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7823  Z= 0.190
  Angle     :  0.630  10.590  10589  Z= 0.326
  Chirality :  0.044   0.232   1201
  Planarity :  0.004   0.042   1339
  Dihedral  :  4.648  20.615   1053
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 26.02 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.63 (0.27), residues: 954
  helix:  1.73 (0.24), residues: 426
  sheet: -0.64 (0.38), residues: 178
  loop : -0.56 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  87 
 HIS   0.009   0.001   HIS A 197 
 PHE   0.019   0.002   PHE B 246 
 TYR   0.011   0.001   TYR A  30 
 ARG   0.007   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  415)
  hydrogen bonds       : angle       4.79301 ( 1203)
  SS BOND              : bond        0.00470 (    2)
  SS BOND              : angle       1.15725 (    4)
  covalent geometry    : bond        0.00411 ( 7821)
  covalent geometry    : angle       0.62974 (10585)

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 254
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7540 (t) cc_final: 0.7299 (p)
REVERT: A   19 ILE cc_start: 0.8349 (tp) cc_final: 0.7881 (tp)
REVERT: A   20 GLU cc_start: 0.7804 (tp30) cc_final: 0.7530 (tp30)
REVERT: A  230 TYR cc_start: 0.8800 (m-10) cc_final: 0.8598 (m-10)
REVERT: A  239 ASP cc_start: 0.8134 (m-30) cc_final: 0.7840 (t0)
REVERT: A  260 LYS cc_start: 0.8688 (mtmp) cc_final: 0.7844 (mtmm)
REVERT: A  267 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8063 (ttpt)
REVERT: A  274 LYS cc_start: 0.8987 (mptt) cc_final: 0.8713 (mptt)
REVERT: A  313 LEU cc_start: 0.8647 (mm) cc_final: 0.8242 (mt)
REVERT: A  321 ASP cc_start: 0.8032 (t0) cc_final: 0.7762 (t0)
REVERT: A  340 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.8164 (tpt170)
REVERT: A  347 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7652 (ttm-80)
REVERT: B   47 ARG cc_start: 0.7829 (ptt-90) cc_final: 0.7598 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7733 (mtt90) cc_final: 0.7304 (mtt90)
REVERT: B   64 TYR cc_start: 0.7953 (m-80) cc_final: 0.7267 (m-80)
REVERT: B   79 SER cc_start: 0.8462 (p) cc_final: 0.7727 (p)
REVERT: B   80 GLN cc_start: 0.7229 (mt0) cc_final: 0.6018 (mt0)
REVERT: B  104 TRP cc_start: 0.8619 (m100) cc_final: 0.7580 (m100)
REVERT: B  115 ASN cc_start: 0.8535 (m110) cc_final: 0.8049 (m110)
REVERT: B  117 VAL cc_start: 0.8799 (p) cc_final: 0.8532 (t)
REVERT: B  142 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7484 (tpp80)
REVERT: B  175 ASP cc_start: 0.7265 (m-30) cc_final: 0.6865 (m-30)
REVERT: B  210 ASP cc_start: 0.7409 (p0) cc_final: 0.7194 (p0)
REVERT: B  222 MET cc_start: 0.7372 (mmm) cc_final: 0.7066 (mmm)
REVERT: B  225 GLN cc_start: 0.8271 (mt0) cc_final: 0.8035 (mt0)
REVERT: B  235 ASN cc_start: 0.8179 (m-40) cc_final: 0.7915 (m110)
REVERT: B  239 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7773 (m-80)
REVERT: B  244 ASN cc_start: 0.8145 (m-40) cc_final: 0.7749 (t0)
REVERT: B  256 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7817 (mtt90)
REVERT: B  263 ASP cc_start: 0.7926 (t0) cc_final: 0.7633 (t70)
REVERT: B  268 THR cc_start: 0.8806 (t) cc_final: 0.8504 (t)
REVERT: B  279 THR cc_start: 0.8440 (m) cc_final: 0.8209 (p)
REVERT: B  309 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8066 (mtm-85)
REVERT: B  338 ASP cc_start: 0.7790 (p0) cc_final: 0.7473 (p0)
REVERT: B  339 SER cc_start: 0.8326 (m) cc_final: 0.7807 (t)
REVERT: R   30 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7228 (tp)
REVERT: R  195 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7285 (t70)
REVERT: R  242 MET cc_start: 0.8249 (ttp) cc_final: 0.7905 (ttp)
REVERT: R  245 CYS cc_start: 0.7746 (p) cc_final: 0.7486 (p)
  outliers start: 31
  outliers final: 23
  residues processed: 269
  average time/residue: 0.2644
  time to fit residues: 89.6015
Evaluate side-chains
  279 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 251
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  186 GLU
Chi-restraints excluded: chain A residue  198 MET
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  267 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 SER
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain B residue  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  234 ILE
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  318 ASN
Chi-restraints excluded: chain P residue   24 ILE
Chi-restraints excluded: chain P residue   52 LEU
Chi-restraints excluded: chain P residue   58 LEU
Chi-restraints excluded: chain R residue   30 ILE
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Chi-restraints excluded: chain R residue  227 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 66 optimal weight:    0.7980
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 318 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.126467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.111122 restraints weight = 11732.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 2.17
r_work: 0.3267 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3102 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7823  Z= 0.176
  Angle     :  0.627  10.540  10589  Z= 0.325
  Chirality :  0.044   0.233   1201
  Planarity :  0.004   0.041   1339
  Dihedral  :  4.689  21.535   1053
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 26.50 %
    Favored  : 69.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.67 (0.27), residues: 954
  helix:  1.75 (0.24), residues: 426
  sheet: -0.64 (0.38), residues: 178
  loop : -0.52 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  87 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.020   0.002   PHE B 246 
 TYR   0.010   0.001   TYR A  30 
 ARG   0.008   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04121 (  415)
  hydrogen bonds       : angle       4.77346 ( 1203)
  SS BOND              : bond        0.00434 (    2)
  SS BOND              : angle       1.03540 (    4)
  covalent geometry    : bond        0.00381 ( 7821)
  covalent geometry    : angle       0.62713 (10585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4804.77 seconds
wall clock time: 84 minutes 12.93 seconds (5052.93 seconds total)