Starting phenix.real_space_refine
on Fri Jun  6 09:35:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hk5_34846/06_2025/8hk5_34846.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hk5_34846/06_2025/8hk5_34846.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hk5_34846/06_2025/8hk5_34846.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hk5_34846/06_2025/8hk5_34846.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hk5_34846/06_2025/8hk5_34846.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hk5_34846/06_2025/8hk5_34846.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    4861      2.51       5
     N    1303      2.21       5
     O    1383      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7604
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2321
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 14, 'TRANS': 278}
    Chain: "B"
      Number of atoms: 573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 573
          Classifications: {'peptide': 74}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 1809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1809
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2509
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "G"
      Number of atoms: 356
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 356
          Classifications: {'peptide': 48}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 4, 'TRANS': 43}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {'PLM': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.55, per 1000 atoms: 0.60
  Number of scatterers: 7604
  At special positions: 0
  Unit cell: (84.048, 99.704, 147.496, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1383      8.00
     N    1303      7.00
     C    4861      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  21 " - pdb=" SG  CYS B  47 " distance=1.99
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  54 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  34 " - pdb=" SG  CYS B  55 " distance=2.05

  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: 1.67
  Conformation dependent library (CDL) restraints added in 952.6 milliseconds
  

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1830

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      47.6% alpha, 18.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 66
    Processing helix  chain 'A' and resid 70 through 88
      removed outlier: 4.331A  pdb=" N   TRP A  74 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A  75 " --> pdb=" O   ASN A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 98
      removed outlier: 3.606A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 140
      Proline residue:  A 113  - end of helix
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 149 through 174
      removed outlier: 3.591A  pdb=" N   ALA A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 195 through 211
    Processing helix  chain 'A' and resid 211 through 231
    Processing helix  chain 'A' and resid 237 through 266
      removed outlier: 4.393A  pdb=" N   LEU A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      Proline residue:  A 257  - end of helix
    Processing helix  chain 'A' and resid 272 through 290
      removed outlier: 3.697A  pdb=" N   LEU A 276 " --> pdb=" O   SER A 272 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   SER A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 5.055A  pdb=" N   LEU A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 304
      removed outlier: 3.938A  pdb=" N   CYS A 294 " --> pdb=" O   TYR A 290 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
    Processing helix  chain 'A' and resid 306 through 314
      removed outlier: 3.706A  pdb=" N   ARG A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 13
      removed outlier: 3.605A  pdb=" N   ILE B   9 " --> pdb=" O   LYS B   5 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LYS B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   TYR B  13 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 27
    Processing helix  chain 'B' and resid 33 through 40
      removed outlier: 4.399A  pdb=" N   ARG B  40 " --> pdb=" O   GLN B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 63
    Processing helix  chain 'C' and resid 6 through 33
      removed outlier: 4.135A  pdb=" N   ALA C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLU C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 53
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 4.248A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   CYS C 214 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 228 through 232
      removed outlier: 3.714A  pdb=" N   LEU C 232 " --> pdb=" O   ASP C 229 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 255
    Processing helix  chain 'C' and resid 270 through 279
      removed outlier: 3.644A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 286
      removed outlier: 3.665A  pdb=" N   ILE C 285 " --> pdb=" O   PRO C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 310
    Processing helix  chain 'C' and resid 330 through 351
    Processing helix  chain 'D' and resid 14 through 26
    Processing helix  chain 'D' and resid 29 through 34
      removed outlier: 3.962A  pdb=" N   ILE D  33 " --> pdb=" O   THR D  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 25
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.548A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 180
    Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 191
      removed outlier: 6.976A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   LEU C  39 " --> pdb=" O   CYS C 224 " (cutoff:3.500A)
      removed outlier: 8.617A  pdb=" N   ALA C 226 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51
      removed outlier: 4.012A  pdb=" N   ARG D  49 " --> pdb=" O   ILE D 338 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   CYS D 317 " --> pdb=" O   GLY D 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63
      removed outlier: 3.632A  pdb=" N   ALA D  60 " --> pdb=" O   ALA D  73 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER D  74 " --> pdb=" O   LYS D  78 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LYS D  78 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU D  79 " --> pdb=" O   ALA D  92 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   ALA D  92 " --> pdb=" O   LEU D  79 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ILE D  81 " --> pdb=" O   VAL D  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105
      removed outlier: 7.193A  pdb=" N   GLY D 115 " --> pdb=" O   MET D 101 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   CYS D 103 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ALA D 113 " --> pdb=" O   CYS D 103 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   TYR D 105 " --> pdb=" O   TYR D 111 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   TYR D 111 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   CYS D 121 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   GLU D 138 " --> pdb=" O   CYS D 121 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ILE D 123 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG D 134 " --> pdb=" O   ASN D 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151
      removed outlier: 3.927A  pdb=" N   THR D 165 " --> pdb=" O   SER D 161 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   ASP D 170 " --> pdb=" O   GLN D 176 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLN D 176 " --> pdb=" O   ASP D 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192
      removed outlier: 6.795A  pdb=" N   GLY D 202 " --> pdb=" O   MET D 188 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   LEU D 190 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   VAL D 200 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   LEU D 192 " --> pdb=" O   LEU D 198 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   LEU D 198 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN D 220 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASP D 212 " --> pdb=" O   CYS D 218 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   CYS D 218 " --> pdb=" O   ASP D 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234
      removed outlier: 6.421A  pdb=" N   GLY D 244 " --> pdb=" O   ASN D 230 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   ILE D 232 " --> pdb=" O   ALA D 242 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ALA D 242 " --> pdb=" O   ILE D 232 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   PHE D 234 " --> pdb=" O   ALA D 240 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   ALA D 240 " --> pdb=" O   PHE D 234 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   MET D 262 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ASP D 254 " --> pdb=" O   GLU D 260 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   GLU D 260 " --> pdb=" O   ASP D 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278
      removed outlier: 6.420A  pdb=" N   GLY D 288 " --> pdb=" O   THR D 274 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   VAL D 276 " --> pdb=" O   LEU D 286 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LEU D 286 " --> pdb=" O   VAL D 276 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   PHE D 278 " --> pdb=" O   LEU D 284 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   LEU D 284 " --> pdb=" O   PHE D 278 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   ASP D 298 " --> pdb=" O   ARG D 304 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   ARG D 304 " --> pdb=" O   ASP D 298 " (cutoff:3.500A)

    399 hydrogen bonds defined for protein.
    1152 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: 2.02

  Time building geometry restraints manager: 2.01 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1239
        1.31 -     1.44: 2067
        1.44 -     1.57: 4372
        1.57 -     1.70: 0
        1.70 -     1.83: 76
  Bond restraints: 7754
  Sorted by residual:
  bond pdb=" CA  TYR B  23 "
       pdb=" C   TYR B  23 "
    ideal  model  delta    sigma   weight residual
    1.524  1.462  0.061 1.29e-02 6.01e+03 2.24e+01
  bond pdb=" C   CYS B  34 "
       pdb=" O   CYS B  34 "
    ideal  model  delta    sigma   weight residual
    1.237  1.187  0.050 1.16e-02 7.43e+03 1.86e+01
  bond pdb=" N   ASP B  24 "
       pdb=" CA  ASP B  24 "
    ideal  model  delta    sigma   weight residual
    1.459  1.407  0.052 1.23e-02 6.61e+03 1.78e+01
  bond pdb=" N   ASP D 291 "
       pdb=" CA  ASP D 291 "
    ideal  model  delta    sigma   weight residual
    1.462  1.417  0.045 1.15e-02 7.56e+03 1.53e+01
  bond pdb=" N   ARG B  37 "
       pdb=" CA  ARG B  37 "
    ideal  model  delta    sigma   weight residual
    1.459  1.414  0.046 1.20e-02 6.94e+03 1.44e+01
  ... (remaining 7749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 10306
        1.47 -     2.95: 135
        2.95 -     4.42: 46
        4.42 -     5.89: 3
        5.89 -     7.37: 5
  Bond angle restraints: 10495
  Sorted by residual:
  angle pdb=" N   GLU A 180 "
        pdb=" CA  GLU A 180 "
        pdb=" C   GLU A 180 "
      ideal   model   delta    sigma   weight residual
     109.24  101.90    7.34 1.63e+00 3.76e-01 2.03e+01
  angle pdb=" N   TYR B  23 "
        pdb=" CA  TYR B  23 "
        pdb=" C   TYR B  23 "
      ideal   model   delta    sigma   weight residual
     111.36  106.58    4.78 1.09e+00 8.42e-01 1.92e+01
  angle pdb=" O   GLU B  32 "
        pdb=" C   GLU B  32 "
        pdb=" N   THR B  33 "
      ideal   model   delta    sigma   weight residual
     123.19  118.62    4.57 1.30e+00 5.92e-01 1.24e+01
  angle pdb=" CA  GLU B  32 "
        pdb=" C   GLU B  32 "
        pdb=" N   THR B  33 "
      ideal   model   delta    sigma   weight residual
     115.63  120.52   -4.89 1.51e+00 4.39e-01 1.05e+01
  angle pdb=" CA  CYS B  55 "
        pdb=" CB  CYS B  55 "
        pdb=" SG  CYS B  55 "
      ideal   model   delta    sigma   weight residual
     114.40  121.77   -7.37 2.30e+00 1.89e-01 1.03e+01
  ... (remaining 10490 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 4293
       16.04 -    32.08: 278
       32.08 -    48.12: 51
       48.12 -    64.17: 13
       64.17 -    80.21: 7
  Dihedral angle restraints: 4642
    sinusoidal: 1826
      harmonic: 2816
  Sorted by residual:
  dihedral pdb=" CA  PHE A 182 "
           pdb=" C   PHE A 182 "
           pdb=" N   PRO A 183 "
           pdb=" CA  PRO A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.88   18.12     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  54 "
           pdb=" CB  CYS B  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -112.86   26.86     1      1.00e+01 1.00e-02 1.04e+01
  dihedral pdb=" CG  ARG B  37 "
           pdb=" CD  ARG B  37 "
           pdb=" NE  ARG B  37 "
           pdb=" CZ  ARG B  37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.02   42.98     2      1.50e+01 4.44e-03 9.92e+00
  ... (remaining 4639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1075
       0.064 -    0.128: 128
       0.128 -    0.192: 4
       0.192 -    0.256: 0
       0.256 -    0.320: 2
  Chirality restraints: 1209
  Sorted by residual:
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CA  CYS B  22 "
            pdb=" N   CYS B  22 "
            pdb=" C   CYS B  22 "
            pdb=" CB  CYS B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CB  THR C 329 "
            pdb=" CA  THR C 329 "
            pdb=" OG1 THR C 329 "
            pdb=" CG2 THR C 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 6.90e-01
  ... (remaining 1206 not shown)

  Planarity restraints: 1319
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 310 "   -0.192 9.50e-02 1.11e+02   8.61e-02 4.55e+00
        pdb=" NE  ARG A 310 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 310 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 310 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 310 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B  21 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.14e+00
        pdb=" C   CYS B  21 "    0.025 2.00e-02 2.50e+03
        pdb=" O   CYS B  21 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   CYS B  22 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  32 "    0.006 2.00e-02 2.50e+03   1.14e-02 1.29e+00
        pdb=" C   GLU B  32 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   GLU B  32 "    0.007 2.00e-02 2.50e+03
        pdb=" N   THR B  33 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1316 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 91
        2.64 -     3.20: 7100
        3.20 -     3.77: 11623
        3.77 -     4.33: 16324
        4.33 -     4.90: 26972
  Nonbonded interactions: 62110
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.073 3.040
  nonbonded pdb=" OG  SER D 147 "
            pdb=" O   MET D 188 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG1 THR D 274 "
            pdb=" OD1 ASP D 290 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OD1 ASP C 251 "
            pdb=" ND2 ASN C 255 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" OH  TYR A 300 "
            pdb=" NH1 ARG A 310 "
     model   vdw
     2.249 3.120
  ... (remaining 62105 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.520
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
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      :  0.003   0.061   7757  Z= 0.219
  Angle     :  0.630  33.924  10501  Z= 0.356
  Chirality :  0.040   0.320   1209
  Planarity :  0.003   0.086   1319
  Dihedral  : 11.846  80.207   2803
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.63 %
    Favored  : 95.13 %
  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: -0.35 (0.26), residues: 955
  helix:  0.58 (0.24), residues: 436
  sheet: -0.04 (0.38), residues: 189
  loop : -1.36 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A  74 
 HIS   0.001   0.000   HIS A 101 
 PHE   0.015   0.001   PHE D 234 
 TYR   0.005   0.000   TYR C 296 
 ARG   0.002   0.000   ARG A 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15119 (  399)
  hydrogen bonds       : angle       5.85674 ( 1152)
  SS BOND              : bond        0.02601 (    3)
  SS BOND              : angle      15.80720 (    6)
  covalent geometry    : bond        0.00315 ( 7754)
  covalent geometry    : angle       0.50461 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 232
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7915 (tpp80)
REVERT: A  298 ILE cc_start: 0.8483 (mt) cc_final: 0.8230 (mp)
REVERT: C  209 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7553 (ttpt)
REVERT: D   82 TRP cc_start: 0.8506 (m100) cc_final: 0.8273 (m100)
REVERT: D   86 THR cc_start: 0.8091 (p) cc_final: 0.7834 (p)
REVERT: D  217 MET cc_start: 0.5944 (ttm) cc_final: 0.5647 (ttm)
REVERT: D  273 ILE cc_start: 0.7134 (mt) cc_final: 0.6924 (mt)
REVERT: D  303 ASP cc_start: 0.6706 (m-30) cc_final: 0.6455 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 234
  average time/residue: 0.9768
  time to fit residues: 243.6810
Evaluate side-chains
  179 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
A 194 HIS
B  67 HIS
D 142 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.134758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.118695 restraints weight = 10325.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.76
r_work: 0.3470 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7757  Z= 0.195
  Angle     :  0.595   7.739  10501  Z= 0.306
  Chirality :  0.043   0.142   1209
  Planarity :  0.004   0.033   1319
  Dihedral  :  4.557  46.812   1069
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.98 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 955
  helix:  1.45 (0.24), residues: 436
  sheet:  0.33 (0.37), residues: 189
  loop : -0.79 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 169 
 HIS   0.011   0.002   HIS B  67 
 PHE   0.019   0.002   PHE D 253 
 TYR   0.020   0.002   TYR A 258 
 ARG   0.007   0.001   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04997 (  399)
  hydrogen bonds       : angle       4.83032 ( 1152)
  SS BOND              : bond        0.00475 (    3)
  SS BOND              : angle       1.89459 (    6)
  covalent geometry    : bond        0.00432 ( 7754)
  covalent geometry    : angle       0.59309 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 0.830 
Fit side-chains
REVERT: B   40 ARG cc_start: 0.7543 (pmm-80) cc_final: 0.7334 (pmm-80)
REVERT: C   29 LYS cc_start: 0.8343 (tppp) cc_final: 0.8046 (mtpp)
REVERT: C  197 LYS cc_start: 0.8253 (tttt) cc_final: 0.7985 (tttm)
REVERT: C  209 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7858 (ttpt)
REVERT: C  216 GLU cc_start: 0.7799 (tt0) cc_final: 0.7597 (tt0)
REVERT: C  334 PHE cc_start: 0.8405 (t80) cc_final: 0.8103 (t80)
REVERT: D  136 SER cc_start: 0.8643 (t) cc_final: 0.8427 (p)
REVERT: D  197 ARG cc_start: 0.7942 (mtp85) cc_final: 0.7718 (mtp180)
REVERT: D  246 ASP cc_start: 0.8163 (m-30) cc_final: 0.7959 (m-30)
REVERT: D  270 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8026 (pp)
REVERT: D  303 ASP cc_start: 0.7588 (m-30) cc_final: 0.7245 (m-30)
REVERT: D  304 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7809 (mmm-85)
  outliers start: 19
  outliers final: 4
  residues processed: 201
  average time/residue: 1.0805
  time to fit residues: 230.8917
Evaluate side-chains
  188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 183
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 79 optimal weight:    0.1980
   chunk 28 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  67 HIS
C 188 HIS
C 269 ASN
D 239 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.136324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.119484 restraints weight = 10532.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.84
r_work: 0.3446 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7757  Z= 0.163
  Angle     :  0.556   7.566  10501  Z= 0.285
  Chirality :  0.042   0.143   1209
  Planarity :  0.004   0.071   1319
  Dihedral  :  4.527  44.169   1069
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.27 %
    Favored  : 78.68 %
  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:  1.00 (0.27), residues: 955
  helix:  1.79 (0.24), residues: 432
  sheet:  0.47 (0.37), residues: 191
  loop : -0.70 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  74 
 HIS   0.009   0.001   HIS B  67 
 PHE   0.014   0.002   PHE C 196 
 TYR   0.016   0.002   TYR A 258 
 ARG   0.011   0.001   ARG B  62 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  399)
  hydrogen bonds       : angle       4.74544 ( 1152)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       1.40156 (    6)
  covalent geometry    : bond        0.00366 ( 7754)
  covalent geometry    : angle       0.55539 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  110 SER cc_start: 0.7920 (m) cc_final: 0.7716 (t)
REVERT: A  167 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7638 (mt)
REVERT: A  236 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7472 (ttp80)
REVERT: A  272 SER cc_start: 0.8711 (t) cc_final: 0.8412 (p)
REVERT: B   40 ARG cc_start: 0.7657 (pmm-80) cc_final: 0.7452 (pmm-80)
REVERT: C   29 LYS cc_start: 0.8348 (tppp) cc_final: 0.8100 (mtpp)
REVERT: C  197 LYS cc_start: 0.8250 (tttt) cc_final: 0.7942 (tttm)
REVERT: C  209 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7843 (ttpt)
REVERT: C  216 GLU cc_start: 0.7812 (tt0) cc_final: 0.7585 (tt0)
REVERT: C  268 LEU cc_start: 0.7859 (mt) cc_final: 0.7644 (mm)
REVERT: C  277 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7929 (ttmt)
REVERT: C  308 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7616 (mt-10)
REVERT: D  136 SER cc_start: 0.8709 (t) cc_final: 0.8477 (p)
REVERT: D  163 ASP cc_start: 0.7772 (p0) cc_final: 0.7509 (p0)
REVERT: D  197 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7791 (mtp180)
REVERT: D  246 ASP cc_start: 0.8189 (m-30) cc_final: 0.7894 (m-30)
REVERT: D  303 ASP cc_start: 0.7579 (m-30) cc_final: 0.7216 (m-30)
  outliers start: 25
  outliers final: 13
  residues processed: 197
  average time/residue: 1.0754
  time to fit residues: 224.6013
Evaluate side-chains
  188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 173
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  186 ASP
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  237 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 90 optimal weight:    7.9990
   chunk 86 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
B  29 ASN
C 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.132017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.115318 restraints weight = 10401.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.83
r_work: 0.3393 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   7757  Z= 0.289
  Angle     :  0.631   8.439  10501  Z= 0.327
  Chirality :  0.046   0.145   1209
  Planarity :  0.004   0.048   1319
  Dihedral  :  4.993  42.379   1069
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 17.78 %
    Favored  : 77.83 %
  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 (0.27), residues: 955
  helix:  1.59 (0.24), residues: 430
  sheet:  0.40 (0.37), residues: 183
  loop : -0.68 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  74 
 HIS   0.006   0.002   HIS C 322 
 PHE   0.022   0.003   PHE D 235 
 TYR   0.025   0.002   TYR A 258 
 ARG   0.011   0.001   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05651 (  399)
  hydrogen bonds       : angle       5.02785 ( 1152)
  SS BOND              : bond        0.00376 (    3)
  SS BOND              : angle       1.42393 (    6)
  covalent geometry    : bond        0.00663 ( 7754)
  covalent geometry    : angle       0.63032 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 178
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A  110 SER cc_start: 0.8037 (m) cc_final: 0.7800 (t)
REVERT: A  236 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7577 (ttp80)
REVERT: A  265 MET cc_start: 0.8432 (mtt) cc_final: 0.8219 (mtt)
REVERT: A  272 SER cc_start: 0.8779 (t) cc_final: 0.8561 (p)
REVERT: A  279 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8181 (mmmm)
REVERT: C   29 LYS cc_start: 0.8421 (tppp) cc_final: 0.8152 (mtpp)
REVERT: C  197 LYS cc_start: 0.8260 (tttt) cc_final: 0.7963 (tttm)
REVERT: C  209 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7848 (ttpt)
REVERT: C  263 SER cc_start: 0.8313 (p) cc_final: 0.8099 (p)
REVERT: C  330 LYS cc_start: 0.7989 (mttt) cc_final: 0.7640 (mtmm)
REVERT: D   33 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.5848 (mt)
REVERT: D  170 ASP cc_start: 0.7827 (m-30) cc_final: 0.7317 (p0)
REVERT: D  213 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7862 (t)
REVERT: D  290 ASP cc_start: 0.6848 (m-30) cc_final: 0.6486 (m-30)
REVERT: D  303 ASP cc_start: 0.7528 (m-30) cc_final: 0.7141 (m-30)
  outliers start: 36
  outliers final: 18
  residues processed: 198
  average time/residue: 1.0293
  time to fit residues: 216.5310
Evaluate side-chains
  188 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain B residue   35 GLU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain D residue   33 ILE
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue   98 SER
Chi-restraints excluded: chain D residue  100 VAL
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  186 ASP
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 79 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  29 ASN
C 188 HIS
D 230 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.135621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.118976 restraints weight = 10171.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 1.80
r_work: 0.3448 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7757  Z= 0.140
  Angle     :  0.538   7.368  10501  Z= 0.278
  Chirality :  0.041   0.140   1209
  Planarity :  0.004   0.044   1319
  Dihedral  :  4.588  39.231   1069
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.51 %
    Favored  : 77.47 %
  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:  1.03 (0.27), residues: 955
  helix:  1.88 (0.25), residues: 430
  sheet:  0.38 (0.37), residues: 183
  loop : -0.66 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  74 
 HIS   0.003   0.001   HIS C 322 
 PHE   0.016   0.002   PHE A 275 
 TYR   0.015   0.002   TYR D  59 
 ARG   0.007   0.000   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04584 (  399)
  hydrogen bonds       : angle       4.75953 ( 1152)
  SS BOND              : bond        0.00241 (    3)
  SS BOND              : angle       1.28320 (    6)
  covalent geometry    : bond        0.00311 ( 7754)
  covalent geometry    : angle       0.53752 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 182
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8219 (mp) cc_final: 0.8001 (mt)
REVERT: A  110 SER cc_start: 0.7946 (m) cc_final: 0.7546 (t)
REVERT: A  236 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7486 (ttp80)
REVERT: A  272 SER cc_start: 0.8793 (t) cc_final: 0.8513 (p)
REVERT: A  279 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8089 (mmmm)
REVERT: C   29 LYS cc_start: 0.8368 (tppp) cc_final: 0.8103 (mtpp)
REVERT: C  197 LYS cc_start: 0.8267 (tttt) cc_final: 0.7988 (tttm)
REVERT: C  209 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7817 (ttpt)
REVERT: C  263 SER cc_start: 0.8283 (p) cc_final: 0.8078 (p)
REVERT: C  277 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7859 (ttmt)
REVERT: C  330 LYS cc_start: 0.7915 (mttt) cc_final: 0.7626 (mttp)
REVERT: D  136 SER cc_start: 0.8713 (t) cc_final: 0.8501 (p)
REVERT: D  170 ASP cc_start: 0.7792 (m-30) cc_final: 0.7317 (p0)
REVERT: D  197 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7776 (mtp180)
REVERT: D  290 ASP cc_start: 0.6847 (m-30) cc_final: 0.6512 (m-30)
REVERT: D  303 ASP cc_start: 0.7440 (m-30) cc_final: 0.7034 (m-30)
  outliers start: 33
  outliers final: 18
  residues processed: 199
  average time/residue: 1.0420
  time to fit residues: 220.5477
Evaluate side-chains
  197 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 178
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  194 HIS
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue   98 SER
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  186 ASP
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  237 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0980
   chunk 27 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 90 optimal weight:    8.9990
   chunk 64 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  29 ASN
C 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.135831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.119161 restraints weight = 10162.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.80
r_work: 0.3443 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7757  Z= 0.137
  Angle     :  0.530   7.678  10501  Z= 0.275
  Chirality :  0.041   0.144   1209
  Planarity :  0.004   0.041   1319
  Dihedral  :  4.480  37.796   1069
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.24 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 955
  helix:  1.94 (0.25), residues: 431
  sheet:  0.35 (0.37), residues: 184
  loop : -0.62 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  74 
 HIS   0.003   0.001   HIS C 322 
 PHE   0.013   0.002   PHE A 275 
 TYR   0.013   0.001   TYR A 300 
 ARG   0.007   0.001   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04540 (  399)
  hydrogen bonds       : angle       4.69652 ( 1152)
  SS BOND              : bond        0.00390 (    3)
  SS BOND              : angle       1.23188 (    6)
  covalent geometry    : bond        0.00302 ( 7754)
  covalent geometry    : angle       0.52907 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8211 (mp) cc_final: 0.7991 (mt)
REVERT: A  110 SER cc_start: 0.8048 (m) cc_final: 0.7795 (t)
REVERT: A  236 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7506 (ttp80)
REVERT: A  279 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8137 (mmmm)
REVERT: C   29 LYS cc_start: 0.8378 (tppp) cc_final: 0.8099 (mtpp)
REVERT: C  197 LYS cc_start: 0.8258 (tttt) cc_final: 0.7984 (tttm)
REVERT: C  209 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7800 (ttpt)
REVERT: C  277 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7814 (ttmt)
REVERT: C  309 ASP cc_start: 0.7303 (m-30) cc_final: 0.6777 (m-30)
REVERT: C  330 LYS cc_start: 0.7912 (mttt) cc_final: 0.7619 (mttp)
REVERT: D  170 ASP cc_start: 0.7784 (m-30) cc_final: 0.7315 (p0)
REVERT: D  197 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7804 (mtp180)
REVERT: D  210 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8045 (tp)
REVERT: D  270 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8010 (mm)
REVERT: D  290 ASP cc_start: 0.6851 (m-30) cc_final: 0.6498 (m-30)
REVERT: D  303 ASP cc_start: 0.7404 (m-30) cc_final: 0.6994 (m-30)
  outliers start: 30
  outliers final: 18
  residues processed: 196
  average time/residue: 1.0134
  time to fit residues: 211.4914
Evaluate side-chains
  195 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  325 CYS
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  186 ASP
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  237 ASN
Chi-restraints excluded: chain D residue  270 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0670
   chunk 73 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 86 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0870
   overall best weight:    0.5096

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

Flipped N/Q/H residues before XYZ refinement:
B  29 ASN
C 188 HIS
D 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.136299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.119587 restraints weight = 10265.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 1.81
r_work: 0.3461 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7757  Z= 0.122
  Angle     :  0.518   7.367  10501  Z= 0.270
  Chirality :  0.040   0.144   1209
  Planarity :  0.003   0.039   1319
  Dihedral  :  4.333  35.279   1069
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.34 %
    Favored  : 76.37 %
  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:  1.18 (0.27), residues: 955
  helix:  2.08 (0.25), residues: 431
  sheet:  0.38 (0.37), residues: 181
  loop : -0.66 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  74 
 HIS   0.003   0.001   HIS C 322 
 PHE   0.021   0.002   PHE C 336 
 TYR   0.012   0.001   TYR A 300 
 ARG   0.008   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  399)
  hydrogen bonds       : angle       4.61607 ( 1152)
  SS BOND              : bond        0.00384 (    3)
  SS BOND              : angle       1.18124 (    6)
  covalent geometry    : bond        0.00264 ( 7754)
  covalent geometry    : angle       0.51724 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 187
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8187 (mp) cc_final: 0.7974 (mt)
REVERT: A  236 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.6841 (ttp80)
REVERT: B   29 ASN cc_start: 0.7689 (t0) cc_final: 0.7422 (t0)
REVERT: C   29 LYS cc_start: 0.8384 (tppp) cc_final: 0.8094 (mtpp)
REVERT: C  186 GLU cc_start: 0.7611 (pt0) cc_final: 0.7387 (pt0)
REVERT: C  188 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.8144 (m170)
REVERT: C  197 LYS cc_start: 0.8251 (tttt) cc_final: 0.7997 (mtpp)
REVERT: C  209 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7778 (ttpt)
REVERT: C  216 GLU cc_start: 0.7779 (tt0) cc_final: 0.7560 (tt0)
REVERT: C  277 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7830 (ttmt)
REVERT: C  308 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7645 (mt-10)
REVERT: C  309 ASP cc_start: 0.7319 (m-30) cc_final: 0.6808 (m-30)
REVERT: C  330 LYS cc_start: 0.7890 (mttt) cc_final: 0.7611 (mttp)
REVERT: D  170 ASP cc_start: 0.7767 (m-30) cc_final: 0.7325 (p0)
REVERT: D  290 ASP cc_start: 0.6838 (m-30) cc_final: 0.6502 (m-30)
REVERT: D  303 ASP cc_start: 0.7373 (m-30) cc_final: 0.7008 (m-30)
  outliers start: 27
  outliers final: 14
  residues processed: 200
  average time/residue: 1.0914
  time to fit residues: 231.6480
Evaluate side-chains
  195 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 179
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  188 HIS
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  237 ASN
Chi-restraints excluded: chain D residue  334 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 92 optimal weight:    0.0670
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0070
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
C 188 HIS
D 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.137032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.120259 restraints weight = 10307.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 1.81
r_work: 0.3460 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7757  Z= 0.125
  Angle     :  0.527   7.472  10501  Z= 0.273
  Chirality :  0.040   0.142   1209
  Planarity :  0.003   0.039   1319
  Dihedral  :  4.315  33.954   1069
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 21.32 %
    Favored  : 75.03 %
  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:  1.20 (0.27), residues: 955
  helix:  2.11 (0.25), residues: 431
  sheet:  0.31 (0.38), residues: 183
  loop : -0.63 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  74 
 HIS   0.007   0.001   HIS C 188 
 PHE   0.018   0.002   PHE C 336 
 TYR   0.016   0.001   TYR C 320 
 ARG   0.006   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  399)
  hydrogen bonds       : angle       4.59532 ( 1152)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       1.19240 (    6)
  covalent geometry    : bond        0.00276 ( 7754)
  covalent geometry    : angle       0.52596 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 179
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8194 (mp) cc_final: 0.7971 (mt)
REVERT: A  236 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6853 (ttp80)
REVERT: B   29 ASN cc_start: 0.7690 (t0) cc_final: 0.7453 (t0)
REVERT: C   29 LYS cc_start: 0.8373 (tppp) cc_final: 0.8088 (mtpp)
REVERT: C  197 LYS cc_start: 0.8261 (tttt) cc_final: 0.7961 (mtpp)
REVERT: C  209 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7783 (ttpt)
REVERT: C  277 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7754 (ttmt)
REVERT: C  330 LYS cc_start: 0.7891 (mttt) cc_final: 0.7616 (mttp)
REVERT: D  101 MET cc_start: 0.8381 (ptm) cc_final: 0.8173 (ptp)
REVERT: D  170 ASP cc_start: 0.7753 (m-30) cc_final: 0.7335 (p0)
REVERT: D  210 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8022 (tp)
REVERT: D  290 ASP cc_start: 0.6865 (m-30) cc_final: 0.6540 (m-30)
REVERT: D  303 ASP cc_start: 0.7359 (m-30) cc_final: 0.6994 (m-30)
  outliers start: 30
  outliers final: 16
  residues processed: 196
  average time/residue: 1.0481
  time to fit residues: 218.5132
Evaluate side-chains
  192 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 SER
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  237 ASN
Chi-restraints excluded: chain D residue  334 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0020
   chunk 4 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8790

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

Flipped N/Q/H residues before XYZ refinement:
C 188 HIS
D 110 ASN
D 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.135629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.118860 restraints weight = 10314.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.81
r_work: 0.3447 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7757  Z= 0.162
  Angle     :  0.575   9.881  10501  Z= 0.295
  Chirality :  0.041   0.140   1209
  Planarity :  0.004   0.040   1319
  Dihedral  :  4.427  31.904   1069
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.92 %
    Favored  : 74.91 %
  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:  1.15 (0.27), residues: 955
  helix:  2.02 (0.24), residues: 432
  sheet:  0.40 (0.38), residues: 182
  loop : -0.65 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  74 
 HIS   0.003   0.001   HIS C 322 
 PHE   0.018   0.002   PHE C 336 
 TYR   0.014   0.002   TYR A 258 
 ARG   0.009   0.001   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04637 (  399)
  hydrogen bonds       : angle       4.67915 ( 1152)
  SS BOND              : bond        0.00482 (    3)
  SS BOND              : angle       1.24738 (    6)
  covalent geometry    : bond        0.00366 ( 7754)
  covalent geometry    : angle       0.57471 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 178
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8261 (mp) cc_final: 0.8027 (mt)
REVERT: A  236 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6916 (ttp80)
REVERT: C   29 LYS cc_start: 0.8397 (tppp) cc_final: 0.8098 (mtpp)
REVERT: C  197 LYS cc_start: 0.8266 (tttt) cc_final: 0.7976 (tttm)
REVERT: C  209 LYS cc_start: 0.8140 (ttpt) cc_final: 0.7798 (ttpt)
REVERT: C  277 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7769 (ttmt)
REVERT: C  330 LYS cc_start: 0.7889 (mttt) cc_final: 0.7622 (mttp)
REVERT: D  101 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8264 (ptp)
REVERT: D  170 ASP cc_start: 0.7745 (m-30) cc_final: 0.7331 (p0)
REVERT: D  210 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8016 (tp)
REVERT: D  290 ASP cc_start: 0.6935 (m-30) cc_final: 0.6609 (m-30)
REVERT: D  303 ASP cc_start: 0.7372 (m-30) cc_final: 0.7019 (m-30)
  outliers start: 26
  outliers final: 18
  residues processed: 192
  average time/residue: 1.0839
  time to fit residues: 221.1634
Evaluate side-chains
  197 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue  101 MET
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  237 ASN
Chi-restraints excluded: chain D residue  334 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B   3 GLN
B  29 ASN
D 239 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.135553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.118725 restraints weight = 10290.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 1.80
r_work: 0.3442 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3294 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7757  Z= 0.158
  Angle     :  0.562   8.976  10501  Z= 0.289
  Chirality :  0.041   0.140   1209
  Planarity :  0.003   0.038   1319
  Dihedral  :  4.422  29.282   1069
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.66 %
    Favored  : 74.42 %
  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:  1.13 (0.27), residues: 955
  helix:  1.97 (0.24), residues: 433
  sheet:  0.29 (0.38), residues: 183
  loop : -0.55 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  74 
 HIS   0.003   0.001   HIS C 322 
 PHE   0.017   0.002   PHE C 336 
 TYR   0.015   0.002   TYR C 320 
 ARG   0.005   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04615 (  399)
  hydrogen bonds       : angle       4.68314 ( 1152)
  SS BOND              : bond        0.00370 (    3)
  SS BOND              : angle       1.24621 (    6)
  covalent geometry    : bond        0.00356 ( 7754)
  covalent geometry    : angle       0.56181 (10495)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 183
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.8245 (mp) cc_final: 0.8010 (mt)
REVERT: A  236 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6943 (ttp80)
REVERT: B   29 ASN cc_start: 0.7661 (t0) cc_final: 0.7080 (t0)
REVERT: C   29 LYS cc_start: 0.8384 (tppp) cc_final: 0.8070 (mtpp)
REVERT: C  197 LYS cc_start: 0.8285 (tttt) cc_final: 0.7972 (mtpp)
REVERT: C  209 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7813 (ttpt)
REVERT: C  271 LYS cc_start: 0.8462 (pttt) cc_final: 0.8161 (pttm)
REVERT: C  277 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7810 (ttmt)
REVERT: C  309 ASP cc_start: 0.7277 (m-30) cc_final: 0.6794 (m-30)
REVERT: C  330 LYS cc_start: 0.7905 (mttt) cc_final: 0.7601 (mttm)
REVERT: D  170 ASP cc_start: 0.7765 (m-30) cc_final: 0.7317 (p0)
REVERT: D  210 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8032 (tp)
REVERT: D  290 ASP cc_start: 0.6961 (m-30) cc_final: 0.6647 (m-30)
REVERT: D  303 ASP cc_start: 0.7376 (m-30) cc_final: 0.7006 (m-30)
  outliers start: 24
  outliers final: 18
  residues processed: 195
  average time/residue: 1.1161
  time to fit residues: 231.2011
Evaluate side-chains
  194 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 174
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  169 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  236 ARG
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  275 GLU
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain D residue   65 THR
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  114 CYS
Chi-restraints excluded: chain D residue  128 THR
Chi-restraints excluded: chain D residue  134 ARG
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  210 LEU
Chi-restraints excluded: chain D residue  213 VAL
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  237 ASN
Chi-restraints excluded: chain D residue  334 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
D 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.135071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118251 restraints weight = 10183.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 1.80
r_work: 0.3439 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7757  Z= 0.180
  Angle     :  0.582   8.959  10501  Z= 0.300
  Chirality :  0.042   0.138   1209
  Planarity :  0.004   0.040   1319
  Dihedral  :  4.500  27.468   1069
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.29 %
    Favored  : 74.79 %
  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:  1.09 (0.27), residues: 955
  helix:  1.92 (0.24), residues: 432
  sheet:  0.37 (0.37), residues: 182
  loop : -0.60 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  74 
 HIS   0.004   0.001   HIS C 322 
 PHE   0.017   0.002   PHE A 147 
 TYR   0.016   0.002   TYR A 258 
 ARG   0.005   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04806 (  399)
  hydrogen bonds       : angle       4.75236 ( 1152)
  SS BOND              : bond        0.00402 (    3)
  SS BOND              : angle       1.28683 (    6)
  covalent geometry    : bond        0.00411 ( 7754)
  covalent geometry    : angle       0.58118 (10495)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6245.82 seconds
wall clock time: 107 minutes 28.80 seconds (6448.80 seconds total)