Starting phenix.real_space_refine
on Sun May 11 05:57:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gy7_34371/05_2025/8gy7_34371_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gy7_34371/05_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_34371/05_2025/8gy7_34371.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gy7_34371/05_2025/8gy7_34371.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gy7_34371/05_2025/8gy7_34371_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gy7_34371/05_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-5687/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: 4.29, per 1000 atoms: 0.56
  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.86
  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: 2.34

  Time building geometry restraints manager: 2.19 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:             0.760
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.270
  Find NCS groups from input model:        0.080
  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:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.750
-------------------------------------------------------------------------------
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  : 0.850 
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: 0.2602
  time to fit residues: 85.9282
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  : 0.830 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.110688 restraints weight = 11636.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 2.18
r_work: 0.3254 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
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       1.71791 (    4)
  covalent geometry    : bond        0.00396 ( 7821)
  covalent geometry    : angle       0.65457 (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  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7693 (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: 0.8256 (m-30) cc_final: 0.7943 (t0)
REVERT: A  267 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8100 (ttpt)
REVERT: A  310 ASP cc_start: 0.7547 (m-30) cc_final: 0.7151 (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: 0.8149 (mtm180) cc_final: 0.7942 (mtm180)
REVERT: B   37 GLN cc_start: 0.8431 (pm20) cc_final: 0.7974 (pm20)
REVERT: B   47 ARG cc_start: 0.7775 (ptt-90) cc_final: 0.7354 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7443 (mtt90)
REVERT: B   64 TYR cc_start: 0.8327 (m-80) cc_final: 0.7883 (m-80)
REVERT: B   80 GLN cc_start: 0.7321 (mt0) cc_final: 0.6592 (mt0)
REVERT: B  115 ASN cc_start: 0.8400 (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: 0.7943 (m110)
REVERT: B  255 CYS cc_start: 0.8116 (t) cc_final: 0.7680 (p)
REVERT: B  279 THR cc_start: 0.8458 (m) cc_final: 0.8254 (p)
REVERT: B  309 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.7721 (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: 0.7647 (p0)
REVERT: B  339 SER cc_start: 0.8431 (m) cc_final: 0.8021 (t)
REVERT: B  345 ASN cc_start: 0.7662 (t0) cc_final: 0.6951 (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: 0.2555
  time to fit residues: 89.7483
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  : 0.746 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0170
   chunk 42 optimal weight:    0.0370
   chunk 1 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0570
   chunk 15 optimal weight:    0.4980
   chunk 46 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.2014

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.128686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.112936 restraints weight = 11777.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.21
r_work: 0.3292 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1835

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= 0.122
  Angle     :  0.582   7.693  10589  Z= 0.308
  Chirality :  0.042   0.151   1201
  Planarity :  0.004   0.057   1339
  Dihedral  :  5.048  58.776   1055
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 22.54 %
    Favored  : 73.86 %
  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:  0.82 (0.28), residues: 954
  helix:  1.91 (0.25), residues: 415
  sheet: -0.53 (0.39), residues: 175
  loop : -0.43 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 174 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.016   0.002   PHE B 246 
 TYR   0.011   0.001   TYR A 230 
 ARG   0.007   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04230 (  415)
  hydrogen bonds       : angle       4.91533 ( 1203)
  SS BOND              : bond        0.00590 (    2)
  SS BOND              : angle       1.78518 (    4)
  covalent geometry    : bond        0.00256 ( 7821)
  covalent geometry    : angle       0.58088 (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
  280 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 250
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7640 (t) cc_final: 0.7404 (p)
REVERT: A  230 TYR cc_start: 0.8664 (m-10) cc_final: 0.8366 (m-10)
REVERT: A  239 ASP cc_start: 0.8265 (m-30) cc_final: 0.7958 (t0)
REVERT: A  260 LYS cc_start: 0.8651 (mtmp) cc_final: 0.8167 (ptpp)
REVERT: A  267 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8065 (ttpt)
REVERT: A  274 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8609 (mptt)
REVERT: A  337 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7843 (mt-10)
REVERT: A  340 ARG cc_start: 0.8444 (tpp-160) cc_final: 0.8080 (tpt170)
REVERT: A  347 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.7528 (ttm-80)
REVERT: A  351 GLN cc_start: 0.8499 (mt0) cc_final: 0.8188 (mt0)
REVERT: B   47 ARG cc_start: 0.7703 (ptt-90) cc_final: 0.7327 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7387 (mtt90)
REVERT: B   64 TYR cc_start: 0.8305 (m-80) cc_final: 0.7972 (m-80)
REVERT: B   74 LEU cc_start: 0.8205 (mt) cc_final: 0.7997 (mt)
REVERT: B  104 TRP cc_start: 0.8566 (m100) cc_final: 0.8249 (m100)
REVERT: B  115 ASN cc_start: 0.8454 (m110) cc_final: 0.8013 (m-40)
REVERT: B  116 TYR cc_start: 0.8473 (m-80) cc_final: 0.7863 (m-80)
REVERT: B  117 VAL cc_start: 0.8797 (p) cc_final: 0.8537 (t)
REVERT: B  142 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7312 (tpp80)
REVERT: B  176 ILE cc_start: 0.8521 (mm) cc_final: 0.7512 (mm)
REVERT: B  244 ASN cc_start: 0.8257 (t0) cc_final: 0.8031 (t0)
REVERT: B  255 CYS cc_start: 0.8218 (t) cc_final: 0.7714 (p)
REVERT: B  256 ARG cc_start: 0.8415 (mtt-85) cc_final: 0.7988 (mtt90)
REVERT: B  259 ASP cc_start: 0.7976 (t0) cc_final: 0.7740 (t0)
REVERT: B  279 THR cc_start: 0.8415 (m) cc_final: 0.8188 (p)
REVERT: B  280 SER cc_start: 0.8639 (t) cc_final: 0.8153 (p)
REVERT: B  309 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7666 (mtm-85)
REVERT: B  316 HIS cc_start: 0.7735 (m-70) cc_final: 0.7450 (m-70)
REVERT: B  328 ASP cc_start: 0.8112 (p0) cc_final: 0.7899 (p0)
REVERT: B  336 SER cc_start: 0.8323 (t) cc_final: 0.8014 (t)
REVERT: B  338 ASP cc_start: 0.7984 (p0) cc_final: 0.7590 (p0)
REVERT: B  339 SER cc_start: 0.8357 (m) cc_final: 0.7863 (t)
REVERT: R   53 LYS cc_start: 0.8577 (tppt) cc_final: 0.8121 (ttpt)
REVERT: R  195 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.7322 (t70)
  outliers start: 30
  outliers final: 14
  residues processed: 266
  average time/residue: 0.2522
  time to fit residues: 85.0817
Evaluate side-chains
  262 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 244
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  266 LEU
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   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:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 HIS
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.126614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.110826 restraints weight = 11775.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 2.22
r_work: 0.3261 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1952

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= 0.168
  Angle     :  0.592   8.365  10589  Z= 0.310
  Chirality :  0.042   0.169   1201
  Planarity :  0.004   0.052   1339
  Dihedral  :  4.691  22.167   1053
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.18 %
    Favored  : 73.38 %
  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:  0.68 (0.27), residues: 954
  helix:  1.68 (0.24), residues: 426
  sheet: -0.54 (0.39), residues: 176
  loop : -0.45 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 174 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.011   0.001   TYR A 230 
 ARG   0.004   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  415)
  hydrogen bonds       : angle       4.87533 ( 1203)
  SS BOND              : bond        0.00528 (    2)
  SS BOND              : angle       2.27548 (    4)
  covalent geometry    : bond        0.00357 ( 7821)
  covalent geometry    : angle       0.59052 (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: 37
    poor density    : 254
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7644 (t) cc_final: 0.7383 (p)
REVERT: A   19 ILE cc_start: 0.8339 (tp) cc_final: 0.7845 (tp)
REVERT: A  230 TYR cc_start: 0.8704 (m-10) cc_final: 0.8422 (m-10)
REVERT: A  234 GLN cc_start: 0.8692 (tp40) cc_final: 0.8435 (tp-100)
REVERT: A  239 ASP cc_start: 0.8302 (m-30) cc_final: 0.7995 (t0)
REVERT: A  267 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8064 (ttpt)
REVERT: A  274 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8597 (mptt)
REVERT: A  340 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.8079 (tpt170)
REVERT: A  347 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7632 (ttm-80)
REVERT: B   37 GLN cc_start: 0.8574 (pm20) cc_final: 0.8369 (pm20)
REVERT: B   47 ARG cc_start: 0.7792 (ptt-90) cc_final: 0.7411 (ptt-90)
REVERT: B   57 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7446 (mtt90)
REVERT: B   64 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.8061 (m-80)
REVERT: B  104 TRP cc_start: 0.8571 (m100) cc_final: 0.8281 (m100)
REVERT: B  115 ASN cc_start: 0.8488 (m110) cc_final: 0.7986 (m110)
REVERT: B  116 TYR cc_start: 0.8474 (m-80) cc_final: 0.7783 (m-80)
REVERT: B  117 VAL cc_start: 0.8798 (p) cc_final: 0.8540 (t)
REVERT: B  142 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7438 (tpp80)
REVERT: B  159 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7476 (m-30)
REVERT: B  176 ILE cc_start: 0.8574 (mm) cc_final: 0.7603 (mm)
REVERT: B  235 ASN cc_start: 0.8086 (m-40) cc_final: 0.7825 (m110)
REVERT: B  239 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7796 (m-80)
REVERT: B  255 CYS cc_start: 0.8244 (t) cc_final: 0.7708 (p)
REVERT: B  263 ASP cc_start: 0.8104 (t0) cc_final: 0.7850 (t0)
REVERT: B  279 THR cc_start: 0.8458 (m) cc_final: 0.8217 (p)
REVERT: B  309 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7764 (mtm-85)
REVERT: B  328 ASP cc_start: 0.8097 (p0) cc_final: 0.7878 (p0)
REVERT: B  339 SER cc_start: 0.8402 (m) cc_final: 0.7989 (t)
REVERT: R   53 LYS cc_start: 0.8605 (tppt) cc_final: 0.8133 (ttpt)
REVERT: R   83 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8360 (tp)
REVERT: R  195 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7410 (t70)
REVERT: R  266 MET cc_start: 0.8183 (mmp) cc_final: 0.7902 (mmm)
  outliers start: 37
  outliers final: 17
  residues processed: 270
  average time/residue: 0.2578
  time to fit residues: 87.3464
Evaluate side-chains
  278 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 253
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  159 ASP
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  330 MET
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   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
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:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0060
   chunk 38 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 73 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7396

-------------------------------------------------------------------------------
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 338 ASN
A 351 GLN
B 225 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.125996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.110929 restraints weight = 11783.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.16
r_work: 0.3271 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2079

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= 0.170
  Angle     :  0.591   7.580  10589  Z= 0.310
  Chirality :  0.042   0.177   1201
  Planarity :  0.004   0.048   1339
  Dihedral  :  4.706  22.688   1053
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 22.90 %
    Favored  : 73.26 %
  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:  0.68 (0.27), residues: 954
  helix:  1.70 (0.24), residues: 426
  sheet: -0.53 (0.39), residues: 176
  loop : -0.48 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 174 
 HIS   0.007   0.001   HIS A 197 
 PHE   0.018   0.002   PHE B 246 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.004   0.000   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04209 (  415)
  hydrogen bonds       : angle       4.83269 ( 1203)
  SS BOND              : bond        0.00522 (    2)
  SS BOND              : angle       1.76619 (    4)
  covalent geometry    : bond        0.00363 ( 7821)
  covalent geometry    : angle       0.59047 (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
  288 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 256
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7614 (t) cc_final: 0.7381 (p)
REVERT: A   19 ILE cc_start: 0.8361 (tp) cc_final: 0.7889 (tp)
REVERT: A  230 TYR cc_start: 0.8707 (m-10) cc_final: 0.8438 (m-10)
REVERT: A  239 ASP cc_start: 0.8207 (m-30) cc_final: 0.7892 (t0)
REVERT: A  260 LYS cc_start: 0.8735 (mtmp) cc_final: 0.8030 (mtmm)
REVERT: A  267 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8074 (ttpt)
REVERT: A  274 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8683 (mptt)
REVERT: A  313 LEU cc_start: 0.8658 (mm) cc_final: 0.8269 (mt)
REVERT: A  340 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8131 (tpt170)
REVERT: A  347 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7672 (ttm-80)
REVERT: B   47 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7583 (ptt-90)
REVERT: B   64 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.8014 (m-80)
REVERT: B   79 SER cc_start: 0.8533 (p) cc_final: 0.7474 (p)
REVERT: B  104 TRP cc_start: 0.8574 (m100) cc_final: 0.8235 (m100)
REVERT: B  115 ASN cc_start: 0.8497 (m110) cc_final: 0.7958 (m110)
REVERT: B  117 VAL cc_start: 0.8781 (p) cc_final: 0.8506 (t)
REVERT: B  142 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7397 (tpp80)
REVERT: B  225 GLN cc_start: 0.8255 (mt0) cc_final: 0.7999 (mt0)
REVERT: B  239 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7869 (m-80)
REVERT: B  255 CYS cc_start: 0.8096 (t) cc_final: 0.7728 (p)
REVERT: B  256 ARG cc_start: 0.8332 (mtt-85) cc_final: 0.7637 (mtt180)
REVERT: B  263 ASP cc_start: 0.7824 (t0) cc_final: 0.7611 (t0)
REVERT: B  279 THR cc_start: 0.8411 (m) cc_final: 0.8186 (p)
REVERT: B  309 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.7709 (mtm-85)
REVERT: B  328 ASP cc_start: 0.8083 (p0) cc_final: 0.7868 (p0)
REVERT: B  338 ASP cc_start: 0.7930 (p0) cc_final: 0.7596 (p0)
REVERT: B  339 SER cc_start: 0.8285 (m) cc_final: 0.7849 (t)
REVERT: B  345 ASN cc_start: 0.7697 (t0) cc_final: 0.7126 (m-40)
REVERT: R   53 LYS cc_start: 0.8599 (tppt) cc_final: 0.8108 (ttpt)
REVERT: R  242 MET cc_start: 0.8382 (tmm) cc_final: 0.8097 (ttp)
REVERT: R  266 MET cc_start: 0.8211 (mmp) cc_final: 0.7882 (mmp)
  outliers start: 32
  outliers final: 19
  residues processed: 267
  average time/residue: 0.2680
  time to fit residues: 90.4353
Evaluate side-chains
  273 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 249
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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  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  110 TYR
Chi-restraints excluded: chain B residue  140 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  178 THR
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  330 MET
Chi-restraints excluded: chain P residue   58 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 ASN
** B  80 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 = 0.3626 r_free = 0.3626 target = 0.126069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110924 restraints weight = 11660.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.13
r_work: 0.3271 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.2160

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= 0.175
  Angle     :  0.591   7.701  10589  Z= 0.311
  Chirality :  0.042   0.182   1201
  Planarity :  0.004   0.044   1339
  Dihedral  :  4.747  22.030   1053
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 23.86 %
    Favored  : 71.82 %
  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:  1.66 (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   0.015   0.002   TRP B 174 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.018   0.002   PHE B 246 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.004   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (  415)
  hydrogen bonds       : angle       4.85024 ( 1203)
  SS BOND              : bond        0.00450 (    2)
  SS BOND              : angle       2.38392 (    4)
  covalent geometry    : bond        0.00375 ( 7821)
  covalent geometry    : angle       0.58961 (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
  287 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 251
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7623 (t) cc_final: 0.7400 (p)
REVERT: A   19 ILE cc_start: 0.8379 (tp) cc_final: 0.7910 (tp)
REVERT: A  210 LYS cc_start: 0.8321 (mttm) cc_final: 0.8088 (mmtm)
REVERT: A  230 TYR cc_start: 0.8721 (m-10) cc_final: 0.8427 (m-10)
REVERT: A  234 GLN cc_start: 0.8769 (tp40) cc_final: 0.8486 (tp-100)
REVERT: A  239 ASP cc_start: 0.8209 (m-30) cc_final: 0.7894 (t0)
REVERT: A  260 LYS cc_start: 0.8769 (mtmp) cc_final: 0.7984 (mtmm)
REVERT: A  267 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8064 (ttpt)
REVERT: A  274 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8679 (mptt)
REVERT: A  313 LEU cc_start: 0.8670 (mm) cc_final: 0.8281 (mt)
REVERT: A  340 ARG cc_start: 0.8525 (tpp-160) cc_final: 0.8134 (tpt170)
REVERT: A  347 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7508 (ttm-80)
REVERT: A  351 GLN cc_start: 0.8596 (mt0) cc_final: 0.8328 (mt0)
REVERT: B   37 GLN cc_start: 0.8487 (pm20) cc_final: 0.7977 (pm20)
REVERT: B   47 ARG cc_start: 0.7829 (ptt-90) cc_final: 0.7600 (ptt-90)
REVERT: B   64 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7983 (m-80)
REVERT: B  104 TRP cc_start: 0.8556 (m100) cc_final: 0.8168 (m100)
REVERT: B  115 ASN cc_start: 0.8521 (m110) cc_final: 0.7966 (m110)
REVERT: B  117 VAL cc_start: 0.8796 (p) cc_final: 0.8534 (t)
REVERT: B  142 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7443 (tpp80)
REVERT: B  217 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7622 (t0)
REVERT: B  222 MET cc_start: 0.7372 (mmm) cc_final: 0.7102 (mmm)
REVERT: B  239 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7833 (m-80)
REVERT: B  255 CYS cc_start: 0.8111 (t) cc_final: 0.7732 (p)
REVERT: B  256 ARG cc_start: 0.8356 (mtt-85) cc_final: 0.7934 (mtt90)
REVERT: B  263 ASP cc_start: 0.7868 (t0) cc_final: 0.7564 (t70)
REVERT: B  279 THR cc_start: 0.8411 (m) cc_final: 0.8166 (p)
REVERT: B  309 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7710 (mtm-85)
REVERT: B  328 ASP cc_start: 0.8064 (p0) cc_final: 0.7849 (p0)
REVERT: B  338 ASP cc_start: 0.7880 (p0) cc_final: 0.7611 (p0)
REVERT: B  345 ASN cc_start: 0.7683 (t0) cc_final: 0.7144 (m-40)
REVERT: R   30 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7325 (tp)
REVERT: R   53 LYS cc_start: 0.8574 (tppt) cc_final: 0.8084 (ttpt)
REVERT: R  195 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7324 (t70)
REVERT: R  242 MET cc_start: 0.8375 (tmm) cc_final: 0.8053 (ttp)
REVERT: R  266 MET cc_start: 0.8180 (mmp) cc_final: 0.7878 (mmp)
  outliers start: 36
  outliers final: 25
  residues processed: 267
  average time/residue: 0.2603
  time to fit residues: 87.2803
Evaluate side-chains
  284 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 251
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
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   64 TYR
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  217 ASP
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   50 VAL
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  143 THR
Chi-restraints excluded: chain R residue  184 LEU
Chi-restraints excluded: chain R residue  195 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0170
   chunk 74 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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  49 GLN
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
B 235 ASN
B 318 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.127081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.111800 restraints weight = 11630.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.15
r_work: 0.3287 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2291

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= 0.137
  Angle     :  0.571   7.935  10589  Z= 0.301
  Chirality :  0.041   0.177   1201
  Planarity :  0.004   0.043   1339
  Dihedral  :  4.663  21.958   1053
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 24.46 %
    Favored  : 70.86 %
  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:  1.78 (0.24), residues: 426
  sheet: -0.68 (0.38), residues: 176
  loop : -0.53 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.019   0.001   PHE B 246 
 TYR   0.011   0.001   TYR R  76 
 ARG   0.006   0.000   ARG R  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  415)
  hydrogen bonds       : angle       4.73231 ( 1203)
  SS BOND              : bond        0.00438 (    2)
  SS BOND              : angle       1.85380 (    4)
  covalent geometry    : bond        0.00296 ( 7821)
  covalent geometry    : angle       0.56967 (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
  291 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 252
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   13 VAL cc_start: 0.7578 (t) cc_final: 0.7346 (p)
REVERT: A   19 ILE cc_start: 0.8370 (tp) cc_final: 0.7911 (tp)
REVERT: A  210 LYS cc_start: 0.8277 (mmtm) cc_final: 0.8043 (mttm)
REVERT: A  230 TYR cc_start: 0.8712 (m-10) cc_final: 0.8414 (m-10)
REVERT: A  234 GLN cc_start: 0.8746 (tp40) cc_final: 0.8448 (tp-100)
REVERT: A  239 ASP cc_start: 0.8168 (m-30) cc_final: 0.7861 (t0)
REVERT: A  260 LYS cc_start: 0.8711 (mtmp) cc_final: 0.7918 (mtmm)
REVERT: A  267 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8075 (ttpt)
REVERT: A  274 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8687 (mptt)
REVERT: A  313 LEU cc_start: 0.8649 (mm) cc_final: 0.8246 (mt)
REVERT: A  340 ARG cc_start: 0.8522 (tpp-160) cc_final: 0.8126 (tpt170)
REVERT: A  347 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7495 (ttm-80)
REVERT: A  351 GLN cc_start: 0.8561 (mt0) cc_final: 0.8331 (mt0)
REVERT: B   37 GLN cc_start: 0.8485 (pm20) cc_final: 0.8233 (pm20)
REVERT: B   64 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7924 (m-80)
REVERT: B  104 TRP cc_start: 0.8545 (m100) cc_final: 0.8195 (m100)
REVERT: B  115 ASN cc_start: 0.8549 (m110) cc_final: 0.8054 (m110)
REVERT: B  116 TYR cc_start: 0.8450 (m-80) cc_final: 0.7747 (m-80)
REVERT: B  117 VAL cc_start: 0.8764 (p) cc_final: 0.8526 (t)
REVERT: B  142 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7424 (tpp80)
REVERT: B  222 MET cc_start: 0.7398 (mmm) cc_final: 0.7108 (mmm)
REVERT: B  225 GLN cc_start: 0.8209 (mt0) cc_final: 0.7987 (mt0)
REVERT: B  239 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7817 (m-80)
REVERT: B  256 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.7839 (mtt90)
REVERT: B  263 ASP cc_start: 0.7685 (t0) cc_final: 0.7373 (t70)
REVERT: B  309 ARG cc_start: 0.8299 (mtm-85) cc_final: 0.7797 (mtm-85)
REVERT: B  338 ASP cc_start: 0.7844 (p0) cc_final: 0.7503 (p0)
REVERT: B  339 SER cc_start: 0.8281 (m) cc_final: 0.7792 (t)
REVERT: B  345 ASN cc_start: 0.7626 (t0) cc_final: 0.7159 (m-40)
REVERT: R   30 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7218 (tp)
REVERT: R  195 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7251 (t70)
REVERT: R  242 MET cc_start: 0.8363 (tmm) cc_final: 0.8026 (ttp)
  outliers start: 39
  outliers final: 23
  residues processed: 270
  average time/residue: 0.2468
  time to fit residues: 83.5161
Evaluate side-chains
  278 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 248
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
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   15 GLU
Chi-restraints excluded: chain B residue   50 MET
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  242 ASN
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
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:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   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**
B  80 GLN
R  56 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.126694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.111438 restraints weight = 11867.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.17
r_work: 0.3264 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2331

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= 0.173
  Angle     :  0.595   9.127  10589  Z= 0.312
  Chirality :  0.042   0.195   1201
  Planarity :  0.004   0.044   1339
  Dihedral  :  4.707  22.041   1053
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.22 %
    Favored  : 70.98 %
  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:  0.62 (0.27), residues: 954
  helix:  1.71 (0.24), residues: 426
  sheet: -0.66 (0.37), residues: 178
  loop : -0.55 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.019   0.002   PHE A 189 
 TYR   0.010   0.001   TYR A  30 
 ARG   0.007   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04134 (  415)
  hydrogen bonds       : angle       4.78489 ( 1203)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       1.74228 (    4)
  covalent geometry    : bond        0.00373 ( 7821)
  covalent geometry    : angle       0.59421 (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
  284 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 244
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7599 (t) cc_final: 0.7367 (p)
REVERT: A   19 ILE cc_start: 0.8371 (tp) cc_final: 0.7927 (tp)
REVERT: A   20 GLU cc_start: 0.7813 (tp30) cc_final: 0.7540 (tp30)
REVERT: A  230 TYR cc_start: 0.8758 (m-10) cc_final: 0.8418 (m-10)
REVERT: A  234 GLN cc_start: 0.8758 (tp40) cc_final: 0.8453 (tp-100)
REVERT: A  239 ASP cc_start: 0.8167 (m-30) cc_final: 0.7864 (t0)
REVERT: A  260 LYS cc_start: 0.8703 (mtmp) cc_final: 0.7876 (mtmm)
REVERT: A  267 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8088 (ttpt)
REVERT: A  313 LEU cc_start: 0.8668 (mm) cc_final: 0.8273 (mt)
REVERT: A  340 ARG cc_start: 0.8531 (tpp-160) cc_final: 0.8135 (tpt170)
REVERT: A  347 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7620 (ttm-80)
REVERT: B   64 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7947 (m-80)
REVERT: B  104 TRP cc_start: 0.8561 (m100) cc_final: 0.8198 (m100)
REVERT: B  115 ASN cc_start: 0.8532 (m110) cc_final: 0.8031 (m110)
REVERT: B  117 VAL cc_start: 0.8796 (p) cc_final: 0.8543 (t)
REVERT: B  142 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7494 (tpp80)
REVERT: B  222 MET cc_start: 0.7394 (mmm) cc_final: 0.7076 (mmm)
REVERT: B  235 ASN cc_start: 0.8208 (m-40) cc_final: 0.7968 (m110)
REVERT: B  239 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7789 (m-80)
REVERT: B  255 CYS cc_start: 0.8132 (t) cc_final: 0.7720 (p)
REVERT: B  263 ASP cc_start: 0.7696 (t0) cc_final: 0.7411 (t70)
REVERT: B  309 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7880 (mtm-85)
REVERT: B  338 ASP cc_start: 0.7853 (p0) cc_final: 0.7521 (p0)
REVERT: B  339 SER cc_start: 0.8297 (m) cc_final: 0.7812 (t)
REVERT: R   30 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7261 (tp)
REVERT: R  242 MET cc_start: 0.8380 (tmm) cc_final: 0.8035 (ttp)
  outliers start: 40
  outliers final: 29
  residues processed: 261
  average time/residue: 0.2429
  time to fit residues: 80.0061
Evaluate side-chains
  278 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 244
  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  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   47 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   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  178 THR
Chi-restraints excluded: chain B residue  180 GLN
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  242 ASN
Chi-restraints excluded: chain B residue  264 GLN
Chi-restraints excluded: chain B residue  330 MET
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  143 THR
Chi-restraints excluded: chain R residue  184 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0670
   chunk 88 optimal weight:    0.2980
   chunk 4 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.4118

-------------------------------------------------------------------------------
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 351 GLN
B  93 ASN
B 225 GLN
B 318 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.127630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.112477 restraints weight = 11854.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.19
r_work: 0.3285 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7823  Z= 0.137
  Angle     :  0.604   9.966  10589  Z= 0.318
  Chirality :  0.042   0.248   1201
  Planarity :  0.004   0.043   1339
  Dihedral  :  4.640  21.131   1053
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 25.66 %
    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:  0.72 (0.28), residues: 954
  helix:  1.85 (0.24), residues: 426
  sheet: -0.67 (0.38), residues: 177
  loop : -0.55 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 174 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.020   0.001   PHE B 246 
 TYR   0.010   0.001   TYR R  76 
 ARG   0.007   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03986 (  415)
  hydrogen bonds       : angle       4.72726 ( 1203)
  SS BOND              : bond        0.00370 (    2)
  SS BOND              : angle       1.45865 (    4)
  covalent geometry    : bond        0.00300 ( 7821)
  covalent geometry    : angle       0.60341 (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
  290 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 253
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7610 (t) cc_final: 0.7350 (p)
REVERT: A   19 ILE cc_start: 0.8356 (tp) cc_final: 0.7893 (tp)
REVERT: A   20 GLU cc_start: 0.7797 (tp30) cc_final: 0.7533 (tp30)
REVERT: A  230 TYR cc_start: 0.8712 (m-10) cc_final: 0.8393 (m-10)
REVERT: A  239 ASP cc_start: 0.8142 (m-30) cc_final: 0.7835 (t0)
REVERT: A  260 LYS cc_start: 0.8688 (mtmp) cc_final: 0.7899 (mtmm)
REVERT: A  267 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8091 (ttpt)
REVERT: A  274 LYS cc_start: 0.9011 (mptt) cc_final: 0.8749 (mptt)
REVERT: A  313 LEU cc_start: 0.8614 (mm) cc_final: 0.8204 (mt)
REVERT: A  340 ARG cc_start: 0.8496 (tpp-160) cc_final: 0.8097 (tpt170)
REVERT: A  347 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7643 (ttm-80)
REVERT: B  104 TRP cc_start: 0.8521 (m100) cc_final: 0.8175 (m100)
REVERT: B  115 ASN cc_start: 0.8553 (m110) cc_final: 0.8068 (m-40)
REVERT: B  117 VAL cc_start: 0.8755 (p) cc_final: 0.8532 (t)
REVERT: B  142 ARG cc_start: 0.7957 (tpp80) cc_final: 0.7325 (tpp80)
REVERT: B  176 ILE cc_start: 0.8516 (mm) cc_final: 0.7661 (mm)
REVERT: B  222 MET cc_start: 0.7419 (mmm) cc_final: 0.7158 (mmm)
REVERT: B  239 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7866 (m-80)
REVERT: B  255 CYS cc_start: 0.8163 (t) cc_final: 0.7688 (p)
REVERT: B  256 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7856 (mtt90)
REVERT: B  263 ASP cc_start: 0.7670 (t0) cc_final: 0.7425 (t70)
REVERT: B  268 THR cc_start: 0.8851 (t) cc_final: 0.8538 (t)
REVERT: B  281 VAL cc_start: 0.8765 (p) cc_final: 0.8512 (t)
REVERT: B  309 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.8054 (mtm-85)
REVERT: B  338 ASP cc_start: 0.7866 (p0) cc_final: 0.7559 (p0)
REVERT: B  339 SER cc_start: 0.8266 (m) cc_final: 0.7837 (t)
REVERT: R   30 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: R  195 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7216 (t70)
REVERT: R  242 MET cc_start: 0.8376 (tmm) cc_final: 0.8024 (ttp)
  outliers start: 37
  outliers final: 27
  residues processed: 269
  average time/residue: 0.2555
  time to fit residues: 86.2734
Evaluate side-chains
  281 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 249
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
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  316 SER
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   47 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   92 THR
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  242 ASN
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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 71 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 GLN
B 235 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.125919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.110770 restraints weight = 11907.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.19
r_work: 0.3251 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7823  Z= 0.216
  Angle     :  0.659  10.529  10589  Z= 0.344
  Chirality :  0.045   0.239   1201
  Planarity :  0.004   0.044   1339
  Dihedral  :  4.789  22.285   1053
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 25.78 %
    Favored  : 70.50 %
  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:  0.60 (0.27), residues: 954
  helix:  1.69 (0.24), residues: 426
  sheet: -0.63 (0.39), residues: 172
  loop : -0.59 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  87 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.020   0.002   PHE B 246 
 TYR   0.012   0.001   TYR A  30 
 ARG   0.007   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  415)
  hydrogen bonds       : angle       4.82448 ( 1203)
  SS BOND              : bond        0.00403 (    2)
  SS BOND              : angle       1.40998 (    4)
  covalent geometry    : bond        0.00465 ( 7821)
  covalent geometry    : angle       0.65868 (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
  287 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 256
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.7580 (t) cc_final: 0.7358 (p)
REVERT: A   19 ILE cc_start: 0.8371 (tp) cc_final: 0.7923 (tp)
REVERT: A   20 GLU cc_start: 0.7834 (tp30) cc_final: 0.7562 (tp30)
REVERT: A  230 TYR cc_start: 0.8792 (m-10) cc_final: 0.8523 (m-10)
REVERT: A  234 GLN cc_start: 0.8786 (tp40) cc_final: 0.8562 (tp-100)
REVERT: A  239 ASP cc_start: 0.8193 (m-30) cc_final: 0.7902 (t0)
REVERT: A  260 LYS cc_start: 0.8685 (mtmp) cc_final: 0.7886 (mtmm)
REVERT: A  267 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8136 (ttpt)
REVERT: A  274 LYS cc_start: 0.8979 (mptt) cc_final: 0.8708 (mptt)
REVERT: A  313 LEU cc_start: 0.8684 (mm) cc_final: 0.8284 (mt)
REVERT: A  340 ARG cc_start: 0.8549 (tpp-160) cc_final: 0.8144 (tpt170)
REVERT: A  347 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7717 (ttm-80)
REVERT: B   57 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7385 (mtt90)
REVERT: B   64 TYR cc_start: 0.7927 (m-80) cc_final: 0.7321 (m-80)
REVERT: B  104 TRP cc_start: 0.8561 (m100) cc_final: 0.8360 (m100)
REVERT: B  115 ASN cc_start: 0.8527 (m110) cc_final: 0.8043 (m-40)
REVERT: B  117 VAL cc_start: 0.8805 (p) cc_final: 0.8541 (t)
REVERT: B  142 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7472 (tpp80)
REVERT: B  222 MET cc_start: 0.7448 (mmm) cc_final: 0.7172 (mmm)
REVERT: B  239 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7806 (m-80)
REVERT: B  255 CYS cc_start: 0.8252 (t) cc_final: 0.7650 (p)
REVERT: B  256 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7777 (mtt90)
REVERT: B  263 ASP cc_start: 0.7757 (t0) cc_final: 0.7484 (t70)
REVERT: B  268 THR cc_start: 0.8836 (t) cc_final: 0.8559 (t)
REVERT: B  309 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8044 (mtm-85)
REVERT: B  338 ASP cc_start: 0.7832 (p0) cc_final: 0.7497 (p0)
REVERT: B  339 SER cc_start: 0.8340 (m) cc_final: 0.7908 (t)
REVERT: B  345 ASN cc_start: 0.7777 (t0) cc_final: 0.7303 (p0)
REVERT: R   30 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7268 (tp)
REVERT: R  242 MET cc_start: 0.8386 (tmm) cc_final: 0.8062 (ttp)
  outliers start: 31
  outliers final: 27
  residues processed: 271
  average time/residue: 0.2521
  time to fit residues: 86.4501
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  : 0.867 
-------------------------------------------------------------------------------
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  316 SER
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain B residue   15 GLU
Chi-restraints excluded: chain B residue   47 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  234 ILE
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  242 ASN
Chi-restraints excluded: chain B residue  264 GLN
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   83 LEU
Chi-restraints excluded: chain R residue   89 MET
Chi-restraints excluded: chain R residue  113 SER
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  184 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 93 optimal weight:    0.6980
   chunk 87 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN
A 338 ASN
** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 357 GLN
B 318 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.126433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.111355 restraints weight = 11782.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.17
r_work: 0.3266 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7823  Z= 0.181
  Angle     :  0.643  10.717  10589  Z= 0.335
  Chirality :  0.044   0.233   1201
  Planarity :  0.004   0.044   1339
  Dihedral  :  4.801  21.121   1053
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 26.62 %
    Favored  : 69.54 %
  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:  0.60 (0.27), residues: 954
  helix:  1.73 (0.24), residues: 426
  sheet: -0.62 (0.39), residues: 170
  loop : -0.65 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  87 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.020   0.002   PHE A 189 
 TYR   0.011   0.001   TYR A  30 
 ARG   0.007   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  415)
  hydrogen bonds       : angle       4.85407 ( 1203)
  SS BOND              : bond        0.00515 (    2)
  SS BOND              : angle       2.16561 (    4)
  covalent geometry    : bond        0.00392 ( 7821)
  covalent geometry    : angle       0.64155 (10585)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4448.57 seconds
wall clock time: 77 minutes 47.78 seconds (4667.78 seconds total)