Starting phenix.real_space_refine
on Sun May 11 11:34:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lyb_63525/05_2025/9lyb_63525_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lyb_63525/05_2025/9lyb_63525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lyb_63525/05_2025/9lyb_63525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lyb_63525/05_2025/9lyb_63525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lyb_63525/05_2025/9lyb_63525_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lyb_63525/05_2025/9lyb_63525_neut.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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    5073      2.51       5
     N    1392      2.21       5
     O    1481      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8003
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1958
          Classifications: {'peptide': 240}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2589
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "G"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 431
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "N"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 971
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
    Chain: "R"
      Number of atoms: 2054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 272, 2054
          Classifications: {'peptide': 272}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 260}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   SER N 127 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  SER N 127 " occ=0.50
  Time building chain proxies: 5.00, per 1000 atoms: 0.62
  Number of scatterers: 8003
  At special positions: 0
  Unit cell: (75.92, 98.8, 130, 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    1481      8.00
     N    1392      7.00
     C    5073      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 177 " - pdb=" SG  CYS R 184 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      42.7% alpha, 20.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 40
      removed outlier: 3.617A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.629A  pdb=" N   LEU A  63 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.590A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
      removed outlier: 3.864A  pdb=" N   LYS A 271 " --> pdb=" O   GLN A 267 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ILE A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.117A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 316
      removed outlier: 4.179A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 313 through 316'
    Processing helix  chain 'A' and resid 331 through 350
      removed outlier: 3.855A  pdb=" N   ARG A 342 " --> pdb=" O   LYS A 338 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.634A  pdb=" N   ILE A 383 " --> pdb=" O   CYS A 379 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLN A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   HIS A 387 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 6 through 24
      removed outlier: 4.053A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.802A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.631A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 42 through 68
      removed outlier: 3.753A  pdb=" N   ILE R  49 " --> pdb=" O   VAL R  45 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   SER R  50 " --> pdb=" O   VAL R  46 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ALA R  59 " --> pdb=" O   SER R  55 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   VAL R  61 " --> pdb=" O   GLU R  57 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE R  65 " --> pdb=" O   VAL R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 103
    Processing helix  chain 'R' and resid 105 through 140
    Processing helix  chain 'R' and resid 140 through 145
      removed outlier: 4.527A  pdb=" N   TYR R 145 " --> pdb=" O   ALA R 141 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 150
    Processing helix  chain 'R' and resid 152 through 168
      removed outlier: 4.376A  pdb=" N   GLY R 166 " --> pdb=" O   GLY R 162 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU R 167 " --> pdb=" O   GLY R 163 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 169 through 174
      removed outlier: 3.731A  pdb=" N   ALA R 174 " --> pdb=" O   LEU R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 231
      removed outlier: 3.562A  pdb=" N   LEU R 195 " --> pdb=" O   SER R 191 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   VAL R 197 " --> pdb=" O   ASN R 193 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 243 through 270
      removed outlier: 4.209A  pdb=" N   PHE R 256 " --> pdb=" O   VAL R 252 " (cutoff:3.500A)
      Proline residue:  R 262  - end of helix
    Processing helix  chain 'R' and resid 275 through 298
      removed outlier: 3.894A  pdb=" N   THR R 279 " --> pdb=" O   PRO R 275 " (cutoff:3.500A)
      Proline residue:  R 285  - end of helix
      removed outlier: 4.125A  pdb=" N   SER R 290 " --> pdb=" O   ALA R 286 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   MET R 291 " --> pdb=" O   THR R 287 " (cutoff:3.500A)
      Proline residue:  R 294  - end of helix
    Processing helix  chain 'R' and resid 301 through 314
      removed outlier: 3.512A  pdb=" N   ALA R 310 " --> pdb=" O   LYS R 306 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   CYS R 313 " --> pdb=" O   TRP R 309 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213
      removed outlier: 4.188A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.274A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.647A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.745A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.394A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.854A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER B 161 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.587A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.610A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.663A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.925A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    427 hydrogen bonds defined for protein.
    1221 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: 2.42

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2631
        1.34 -     1.46: 1811
        1.46 -     1.58: 3640
        1.58 -     1.70: 0
        1.70 -     1.81: 78
  Bond restraints: 8160
  Sorted by residual:
  bond pdb=" N   LEU R 142 "
       pdb=" CA  LEU R 142 "
    ideal  model  delta    sigma   weight residual
    1.459  1.480 -0.021 1.23e-02 6.61e+03 2.97e+00
  bond pdb=" N   ASN R 140 "
       pdb=" CA  ASN R 140 "
    ideal  model  delta    sigma   weight residual
    1.462  1.486 -0.024 1.44e-02 4.82e+03 2.73e+00
  bond pdb=" CA  ALA R 141 "
       pdb=" CB  ALA R 141 "
    ideal  model  delta    sigma   weight residual
    1.529  1.504  0.025 1.55e-02 4.16e+03 2.51e+00
  bond pdb=" N   ALA R 141 "
       pdb=" CA  ALA R 141 "
    ideal  model  delta    sigma   weight residual
    1.459  1.475 -0.016 1.19e-02 7.06e+03 1.82e+00
  bond pdb=" CB  ILE R 216 "
       pdb=" CG2 ILE R 216 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  ... (remaining 8155 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 10874
        1.92 -     3.85: 164
        3.85 -     5.77: 29
        5.77 -     7.69: 3
        7.69 -     9.62: 5
  Bond angle restraints: 11075
  Sorted by residual:
  angle pdb=" N   VAL R 150 "
        pdb=" CA  VAL R 150 "
        pdb=" C   VAL R 150 "
      ideal   model   delta    sigma   weight residual
     112.96  106.90    6.06 1.00e+00 1.00e+00 3.67e+01
  angle pdb=" N   VAL R 186 "
        pdb=" CA  VAL R 186 "
        pdb=" C   VAL R 186 "
      ideal   model   delta    sigma   weight residual
     113.43  108.17    5.26 1.09e+00 8.42e-01 2.33e+01
  angle pdb=" CA  MET R 209 "
        pdb=" CB  MET R 209 "
        pdb=" CG  MET R 209 "
      ideal   model   delta    sigma   weight residual
     114.10  122.78   -8.68 2.00e+00 2.50e-01 1.89e+01
  angle pdb=" C   TYR R 188 "
        pdb=" N   PRO R 189 "
        pdb=" CD  PRO R 189 "
      ideal   model   delta    sigma   weight residual
     120.60  112.51    8.09 2.20e+00 2.07e-01 1.35e+01
  angle pdb=" CA  ASN R 140 "
        pdb=" C   ASN R 140 "
        pdb=" O   ASN R 140 "
      ideal   model   delta    sigma   weight residual
     122.51  118.07    4.44 1.34e+00 5.57e-01 1.10e+01
  ... (remaining 11070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 4440
       16.40 -    32.79: 323
       32.79 -    49.19: 77
       49.19 -    65.58: 11
       65.58 -    81.98: 6
  Dihedral angle restraints: 4857
    sinusoidal: 1852
      harmonic: 3005
  Sorted by residual:
  dihedral pdb=" CB  CYS R 177 "
           pdb=" SG  CYS R 177 "
           pdb=" SG  CYS R 184 "
           pdb=" CB  CYS R 184 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.64   72.64     1      1.00e+01 1.00e-02 6.74e+01
  dihedral pdb=" CA  ALA R  42 "
           pdb=" C   ALA R  42 "
           pdb=" N   TRP R  43 "
           pdb=" CA  TRP R  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.28  -19.72     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 4854 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 881
       0.037 -    0.073: 282
       0.073 -    0.110: 90
       0.110 -    0.147: 19
       0.147 -    0.184: 3
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  ASN R 140 "
            pdb=" N   ASN R 140 "
            pdb=" C   ASN R 140 "
            pdb=" CB  ASN R 140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.42e-01
  chirality pdb=" CA  TYR B  59 "
            pdb=" N   TYR B  59 "
            pdb=" C   TYR B  59 "
            pdb=" CB  TYR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.99e-01
  ... (remaining 1272 not shown)

  Planarity restraints: 1411
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR R 188 "   -0.054 5.00e-02 4.00e+02   8.29e-02 1.10e+01
        pdb=" N   PRO R 189 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO R 189 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO R 189 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R 139 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.31e+00
        pdb=" C   TYR R 139 "    0.050 2.00e-02 2.50e+03
        pdb=" O   TYR R 139 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN R 140 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.021 2.00e-02 2.50e+03   1.47e-02 4.35e+00
        pdb=" CG  TYR B  59 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1408 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 115
        2.67 -     3.23: 7531
        3.23 -     3.78: 12342
        3.78 -     4.34: 16719
        4.34 -     4.90: 27538
  Nonbonded interactions: 64245
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" O   ALA R 106 "
            pdb=" OG  SER R 109 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   TYR R 144 "
            pdb=" OG1 THR R 149 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OD1 ASP N  50 "
            pdb=" OG  SER N  59 "
     model   vdw
     2.261 3.040
  ... (remaining 64240 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     21.200
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
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   0.043   8163  Z= 0.138
  Angle     :  0.605   9.616  11081  Z= 0.334
  Chirality :  0.041   0.184   1275
  Planarity :  0.005   0.083   1411
  Dihedral  : 12.555  81.976   2908
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1021
  helix:  1.10 (0.26), residues: 396
  sheet:  0.73 (0.34), residues: 224
  loop : -0.60 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.016   0.001   PHE B 234 
 TYR   0.035   0.001   TYR B  59 
 ARG   0.013   0.001   ARG N 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17762 (  427)
  hydrogen bonds       : angle       6.28508 ( 1221)
  SS BOND              : bond        0.00130 (    3)
  SS BOND              : angle       0.68955 (    6)
  covalent geometry    : bond        0.00279 ( 8160)
  covalent geometry    : angle       0.60474 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 LYS cc_start: 0.8200 (mttm) cc_final: 0.7957 (mttm)
REVERT: A  223 ASP cc_start: 0.6549 (t0) cc_final: 0.6333 (t0)
REVERT: A  231 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7711 (ptp-170)
REVERT: A  278 ASN cc_start: 0.7744 (m-40) cc_final: 0.7415 (m110)
REVERT: A  292 ASN cc_start: 0.8154 (t0) cc_final: 0.7945 (t0)
REVERT: A  386 MET cc_start: 0.7769 (tmm) cc_final: 0.7511 (tmm)
REVERT: B   46 ARG cc_start: 0.6938 (mtm180) cc_final: 0.6644 (mtm180)
REVERT: B   98 SER cc_start: 0.7996 (m) cc_final: 0.7670 (t)
REVERT: B  120 ILE cc_start: 0.7246 (mt) cc_final: 0.7026 (mm)
REVERT: B  125 ASN cc_start: 0.8065 (t0) cc_final: 0.7748 (t0)
REVERT: B  137 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7255 (tpp-160)
REVERT: B  155 ASN cc_start: 0.7803 (t0) cc_final: 0.7386 (t0)
REVERT: B  198 LEU cc_start: 0.8593 (mt) cc_final: 0.8341 (mp)
REVERT: B  230 ASN cc_start: 0.8270 (m-40) cc_final: 0.7858 (m110)
REVERT: B  239 ASN cc_start: 0.7516 (m110) cc_final: 0.6759 (m-40)
REVERT: B  254 ASP cc_start: 0.6764 (t70) cc_final: 0.6064 (t70)
REVERT: B  256 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7070 (mtm180)
REVERT: B  258 ASP cc_start: 0.7001 (t70) cc_final: 0.6761 (t0)
REVERT: B  277 SER cc_start: 0.8054 (p) cc_final: 0.7618 (m)
REVERT: B  295 ASN cc_start: 0.8190 (m-40) cc_final: 0.7927 (m-40)
REVERT: N   46 GLU cc_start: 0.7058 (tt0) cc_final: 0.6844 (tt0)
REVERT: N   50 ASP cc_start: 0.6705 (p0) cc_final: 0.6351 (p0)
REVERT: N  120 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7387 (mm-40)
REVERT: R  108 MET cc_start: 0.4450 (tpp) cc_final: 0.3887 (tpp)
REVERT: R  120 PHE cc_start: 0.8182 (m-10) cc_final: 0.7847 (m-10)
REVERT: R  143 THR cc_start: 0.8242 (m) cc_final: 0.7898 (p)
REVERT: R  188 TYR cc_start: 0.7251 (t80) cc_final: 0.7001 (t80)
REVERT: R  208 ILE cc_start: 0.7936 (mt) cc_final: 0.7697 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.2655
  time to fit residues: 85.9831
Evaluate side-chains
  229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
N  53 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.119276 restraints weight = 11436.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.02
r_work: 0.3352 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3165
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3165 r_free = 0.3165    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3165
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8163  Z= 0.195
  Angle     :  0.622   7.684  11081  Z= 0.328
  Chirality :  0.044   0.166   1275
  Planarity :  0.005   0.053   1411
  Dihedral  :  4.531  20.476   1123
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  :  9.62 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.91 (0.26), residues: 1021
  helix:  1.55 (0.26), residues: 399
  sheet:  0.78 (0.35), residues: 217
  loop : -0.39 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.007   0.001   HIS A 357 
 PHE   0.015   0.002   PHE R  97 
 TYR   0.028   0.002   TYR B  59 
 ARG   0.010   0.001   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  427)
  hydrogen bonds       : angle       4.73504 ( 1221)
  SS BOND              : bond        0.00533 (    3)
  SS BOND              : angle       1.03866 (    6)
  covalent geometry    : bond        0.00438 ( 8160)
  covalent geometry    : angle       0.62191 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 218
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.8016 (p) cc_final: 0.7734 (m)
REVERT: A  211 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7889 (mtpp)
REVERT: A  265 ARG cc_start: 0.7600 (mmp80) cc_final: 0.7350 (mmp80)
REVERT: A  300 LYS cc_start: 0.7484 (mtpt) cc_final: 0.7176 (mtpt)
REVERT: A  343 ASP cc_start: 0.8286 (m-30) cc_final: 0.8021 (m-30)
REVERT: A  376 PHE cc_start: 0.8288 (t80) cc_final: 0.8040 (t80)
REVERT: B   18 ILE cc_start: 0.8730 (mm) cc_final: 0.8514 (mm)
REVERT: B   49 ARG cc_start: 0.8631 (mmt90) cc_final: 0.8425 (mpt180)
REVERT: B   61 MET cc_start: 0.8392 (ppp) cc_final: 0.7627 (ppp)
REVERT: B   98 SER cc_start: 0.8658 (m) cc_final: 0.8252 (t)
REVERT: B  137 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7767 (tpp-160)
REVERT: B  212 ASP cc_start: 0.7598 (m-30) cc_final: 0.6686 (m-30)
REVERT: B  219 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7117 (ttm-80)
REVERT: B  230 ASN cc_start: 0.8512 (m-40) cc_final: 0.8079 (m110)
REVERT: B  256 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.8051 (mtm180)
REVERT: B  258 ASP cc_start: 0.8086 (t70) cc_final: 0.7385 (t0)
REVERT: B  277 SER cc_start: 0.8286 (p) cc_final: 0.7837 (m)
REVERT: G   21 MET cc_start: 0.8303 (tpt) cc_final: 0.8099 (tpt)
REVERT: N   86 LEU cc_start: 0.8739 (mt) cc_final: 0.8536 (mt)
REVERT: N  120 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8238 (mm-40)
REVERT: R   53 LEU cc_start: 0.7318 (mt) cc_final: 0.7087 (mt)
REVERT: R  209 MET cc_start: 0.8479 (tpp) cc_final: 0.8142 (mmt)
REVERT: R  244 LYS cc_start: 0.7799 (tptp) cc_final: 0.7563 (tptp)
REVERT: R  251 VAL cc_start: 0.8309 (t) cc_final: 0.8093 (p)
  outliers start: 16
  outliers final: 8
  residues processed: 224
  average time/residue: 0.2691
  time to fit residues: 75.3451
Evaluate side-chains
  214 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 206
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  118 MET
Chi-restraints excluded: chain R residue  273 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0870
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0060
   chunk 43 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 67 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.3774

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

Flipped N/Q/H residues before XYZ refinement:
N  53 GLN
R  58 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.119309 restraints weight = 11620.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 2.07
r_work: 0.3392 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8163  Z= 0.117
  Angle     :  0.501   7.573  11081  Z= 0.263
  Chirality :  0.040   0.147   1275
  Planarity :  0.004   0.037   1411
  Dihedral  :  4.158  19.839   1123
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 12.91 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: 1021
  helix:  1.87 (0.26), residues: 405
  sheet:  0.62 (0.35), residues: 219
  loop : -0.25 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.009   0.001   PHE R 101 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.004   0.001   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  427)
  hydrogen bonds       : angle       4.41903 ( 1221)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       0.53034 (    6)
  covalent geometry    : bond        0.00251 ( 8160)
  covalent geometry    : angle       0.50067 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 213
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
REVERT: A  292 ASN cc_start: 0.8670 (t0) cc_final: 0.8439 (t0)
REVERT: A  300 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7186 (mtpt)
REVERT: A  376 PHE cc_start: 0.8476 (t80) cc_final: 0.8251 (t80)
REVERT: A  381 ASP cc_start: 0.7837 (t0) cc_final: 0.7533 (t0)
REVERT: B   16 ASN cc_start: 0.8021 (m-40) cc_final: 0.7771 (m-40)
REVERT: B   19 ARG cc_start: 0.7989 (ttp-110) cc_final: 0.7712 (ttp-110)
REVERT: B   49 ARG cc_start: 0.8641 (mmt90) cc_final: 0.8316 (mpt90)
REVERT: B   61 MET cc_start: 0.8345 (ppp) cc_final: 0.7660 (ppp)
REVERT: B   70 LEU cc_start: 0.8704 (pp) cc_final: 0.8448 (pt)
REVERT: B   75 GLN cc_start: 0.8250 (mm110) cc_final: 0.7873 (mm110)
REVERT: B   98 SER cc_start: 0.8755 (m) cc_final: 0.8350 (t)
REVERT: B  137 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7840 (tpp-160)
REVERT: B  212 ASP cc_start: 0.7614 (m-30) cc_final: 0.6784 (m-30)
REVERT: B  230 ASN cc_start: 0.8446 (m-40) cc_final: 0.8046 (m-40)
REVERT: B  258 ASP cc_start: 0.8126 (t70) cc_final: 0.7301 (t70)
REVERT: B  277 SER cc_start: 0.8286 (p) cc_final: 0.7804 (m)
REVERT: B  289 TYR cc_start: 0.8659 (m-80) cc_final: 0.8244 (m-80)
REVERT: G   21 MET cc_start: 0.8225 (tpt) cc_final: 0.8019 (tpt)
REVERT: G   27 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8209 (mtt-85)
REVERT: N   86 LEU cc_start: 0.8742 (mt) cc_final: 0.8541 (mt)
REVERT: N  120 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8101 (mm-40)
REVERT: R   53 LEU cc_start: 0.7374 (mt) cc_final: 0.7109 (mt)
REVERT: R   61 VAL cc_start: 0.8420 (p) cc_final: 0.8176 (t)
REVERT: R  120 PHE cc_start: 0.8674 (m-10) cc_final: 0.8316 (m-10)
REVERT: R  209 MET cc_start: 0.8371 (tpp) cc_final: 0.8107 (mmt)
REVERT: R  251 VAL cc_start: 0.8292 (t) cc_final: 0.8081 (p)
REVERT: R  295 ILE cc_start: 0.8190 (mt) cc_final: 0.7969 (mp)
  outliers start: 14
  outliers final: 6
  residues processed: 216
  average time/residue: 0.3013
  time to fit residues: 80.9133
Evaluate side-chains
  211 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 205
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   33 LYS
Chi-restraints excluded: chain R residue  249 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0770
   chunk 1 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.116416 restraints weight = 11521.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.04
r_work: 0.3340 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3171 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8163  Z= 0.165
  Angle     :  0.543   7.385  11081  Z= 0.286
  Chirality :  0.041   0.142   1275
  Planarity :  0.004   0.038   1411
  Dihedral  :  4.332  19.314   1123
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.97 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.11 (0.26), residues: 1021
  helix:  1.79 (0.26), residues: 409
  sheet:  0.60 (0.35), residues: 211
  loop : -0.22 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.013   0.002   PHE A 212 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.005   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  427)
  hydrogen bonds       : angle       4.47093 ( 1221)
  SS BOND              : bond        0.00198 (    3)
  SS BOND              : angle       2.04969 (    6)
  covalent geometry    : bond        0.00365 ( 8160)
  covalent geometry    : angle       0.54071 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 221
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 THR cc_start: 0.8863 (p) cc_final: 0.8596 (m)
REVERT: A  274 ASP cc_start: 0.8078 (t0) cc_final: 0.7841 (t0)
REVERT: A  292 ASN cc_start: 0.8655 (t0) cc_final: 0.8360 (t0)
REVERT: A  300 LYS cc_start: 0.7545 (mtpt) cc_final: 0.7247 (mtpt)
REVERT: A  372 ILE cc_start: 0.8176 (pt) cc_final: 0.7905 (mm)
REVERT: B    6 GLN cc_start: 0.7088 (pp30) cc_final: 0.6768 (pp30)
REVERT: B   13 GLN cc_start: 0.7789 (pp30) cc_final: 0.7512 (pp30)
REVERT: B   61 MET cc_start: 0.8370 (ppp) cc_final: 0.7721 (ppp)
REVERT: B   70 LEU cc_start: 0.8698 (pp) cc_final: 0.8432 (pt)
REVERT: B   98 SER cc_start: 0.8724 (m) cc_final: 0.8316 (t)
REVERT: B  101 MET cc_start: 0.8285 (mtp) cc_final: 0.8020 (mtp)
REVERT: B  137 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7903 (tpp-160)
REVERT: B  228 ASP cc_start: 0.7917 (m-30) cc_final: 0.7433 (m-30)
REVERT: B  230 ASN cc_start: 0.8410 (m-40) cc_final: 0.8031 (m-40)
REVERT: B  256 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8121 (mtm-85)
REVERT: B  258 ASP cc_start: 0.8136 (t70) cc_final: 0.7531 (t70)
REVERT: B  277 SER cc_start: 0.8290 (p) cc_final: 0.7826 (m)
REVERT: B  289 TYR cc_start: 0.8683 (m-80) cc_final: 0.8236 (m-80)
REVERT: G   20 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8129 (mtmm)
REVERT: G   21 MET cc_start: 0.8258 (tpt) cc_final: 0.8032 (tpt)
REVERT: N  120 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8307 (mm-40)
REVERT: R   53 LEU cc_start: 0.7406 (mt) cc_final: 0.7122 (mt)
REVERT: R   61 VAL cc_start: 0.8446 (p) cc_final: 0.8200 (t)
REVERT: R   72 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7449 (mmm-85)
REVERT: R  118 MET cc_start: 0.8459 (ttm) cc_final: 0.8216 (ttm)
REVERT: R  120 PHE cc_start: 0.8629 (m-10) cc_final: 0.8420 (m-10)
REVERT: R  193 ASN cc_start: 0.7900 (t0) cc_final: 0.7627 (m-40)
REVERT: R  209 MET cc_start: 0.8360 (tpp) cc_final: 0.8068 (mmt)
  outliers start: 19
  outliers final: 13
  residues processed: 228
  average time/residue: 0.2936
  time to fit residues: 82.5360
Evaluate side-chains
  229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 216
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue  159 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  186 VAL
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  273 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 4 optimal weight:    9.9990
   chunk 36 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.111531 restraints weight = 11422.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.07
r_work: 0.3225 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3053
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3053
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.4935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   8163  Z= 0.265
  Angle     :  0.606   8.473  11081  Z= 0.323
  Chirality :  0.044   0.140   1275
  Planarity :  0.004   0.038   1411
  Dihedral  :  4.634  20.816   1123
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.74 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.55 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.93 (0.26), residues: 1021
  helix:  1.74 (0.25), residues: 405
  sheet:  0.28 (0.34), residues: 217
  loop : -0.29 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.009   0.002   HIS A 357 
 PHE   0.017   0.002   PHE A 212 
 TYR   0.018   0.002   TYR B  59 
 ARG   0.004   0.001   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04754 (  427)
  hydrogen bonds       : angle       4.75120 ( 1221)
  SS BOND              : bond        0.00306 (    3)
  SS BOND              : angle       1.37382 (    6)
  covalent geometry    : bond        0.00596 ( 8160)
  covalent geometry    : angle       0.60547 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 218
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7131 (mm-30)
REVERT: A  242 THR cc_start: 0.8840 (p) cc_final: 0.8589 (m)
REVERT: A  248 VAL cc_start: 0.8393 (t) cc_final: 0.8151 (m)
REVERT: A  274 ASP cc_start: 0.8111 (t0) cc_final: 0.7820 (t0)
REVERT: A  292 ASN cc_start: 0.8661 (t0) cc_final: 0.8393 (t0)
REVERT: A  300 LYS cc_start: 0.7590 (mtpt) cc_final: 0.7253 (mtpt)
REVERT: A  347 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7602 (ttp80)
REVERT: A  392 GLU cc_start: 0.7289 (pt0) cc_final: 0.6948 (pt0)
REVERT: B   13 GLN cc_start: 0.7874 (pp30) cc_final: 0.7598 (pp30)
REVERT: B   19 ARG cc_start: 0.8069 (ttp-110) cc_final: 0.7725 (ttp-110)
REVERT: B   59 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8046 (t80)
REVERT: B   61 MET cc_start: 0.8385 (ppp) cc_final: 0.7811 (ppp)
REVERT: B   70 LEU cc_start: 0.8702 (pp) cc_final: 0.8443 (pt)
REVERT: B   87 THR cc_start: 0.8425 (m) cc_final: 0.8178 (t)
REVERT: B   98 SER cc_start: 0.8705 (m) cc_final: 0.8381 (p)
REVERT: B  186 ASP cc_start: 0.7257 (m-30) cc_final: 0.7033 (t0)
REVERT: B  219 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7571 (mmm160)
REVERT: B  230 ASN cc_start: 0.8418 (m-40) cc_final: 0.8009 (m110)
REVERT: B  258 ASP cc_start: 0.8168 (t70) cc_final: 0.7323 (t0)
REVERT: B  277 SER cc_start: 0.8287 (p) cc_final: 0.7816 (m)
REVERT: G   21 MET cc_start: 0.8466 (tpt) cc_final: 0.8207 (tpt)
REVERT: G   27 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8322 (mtt-85)
REVERT: R   48 CYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5536 (t)
REVERT: R   57 GLU cc_start: 0.7799 (tp30) cc_final: 0.7593 (tp30)
REVERT: R   61 VAL cc_start: 0.8477 (p) cc_final: 0.8196 (t)
REVERT: R  118 MET cc_start: 0.8374 (ttm) cc_final: 0.8138 (ttm)
REVERT: R  193 ASN cc_start: 0.7967 (t0) cc_final: 0.7724 (m-40)
REVERT: R  209 MET cc_start: 0.8381 (tpp) cc_final: 0.7867 (mmm)
REVERT: R  249 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7951 (tt)
  outliers start: 27
  outliers final: 14
  residues processed: 226
  average time/residue: 0.2813
  time to fit residues: 79.2633
Evaluate side-chains
  238 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 219
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  280 LYS
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  219 ARG
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   48 CYS
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  273 HIS
Chi-restraints excluded: chain R residue  291 MET
Chi-restraints excluded: chain R residue  300 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 80 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.112894 restraints weight = 11569.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.06
r_work: 0.3251 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.4995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8163  Z= 0.175
  Angle     :  0.531   7.193  11081  Z= 0.283
  Chirality :  0.041   0.127   1275
  Planarity :  0.004   0.038   1411
  Dihedral  :  4.375  18.617   1123
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.45 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.90 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.11 (0.27), residues: 1021
  helix:  1.97 (0.25), residues: 405
  sheet:  0.20 (0.34), residues: 217
  loop : -0.16 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.015   0.002   PHE B 234 
 TYR   0.010   0.001   TYR R 139 
 ARG   0.003   0.000   ARG A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04184 (  427)
  hydrogen bonds       : angle       4.54993 ( 1221)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       0.69703 (    6)
  covalent geometry    : bond        0.00390 ( 8160)
  covalent geometry    : angle       0.53135 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7037 (mm-30)
REVERT: A  242 THR cc_start: 0.8802 (p) cc_final: 0.8564 (m)
REVERT: A  248 VAL cc_start: 0.8410 (t) cc_final: 0.8186 (m)
REVERT: A  274 ASP cc_start: 0.8074 (t0) cc_final: 0.7763 (t0)
REVERT: A  292 ASN cc_start: 0.8653 (t0) cc_final: 0.8367 (t0)
REVERT: A  300 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7254 (mtpt)
REVERT: A  392 GLU cc_start: 0.7190 (pt0) cc_final: 0.6875 (pt0)
REVERT: B   13 GLN cc_start: 0.7883 (pp30) cc_final: 0.7585 (pp30)
REVERT: B   23 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8369 (ttpt)
REVERT: B   59 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8050 (t80)
REVERT: B   61 MET cc_start: 0.8375 (ppp) cc_final: 0.7876 (ppp)
REVERT: B   70 LEU cc_start: 0.8670 (pp) cc_final: 0.8411 (pt)
REVERT: B   98 SER cc_start: 0.8598 (m) cc_final: 0.8302 (p)
REVERT: B  170 ASP cc_start: 0.7986 (t70) cc_final: 0.7712 (t0)
REVERT: B  228 ASP cc_start: 0.7956 (m-30) cc_final: 0.7747 (m-30)
REVERT: B  230 ASN cc_start: 0.8358 (m-40) cc_final: 0.7972 (m-40)
REVERT: B  258 ASP cc_start: 0.8173 (t70) cc_final: 0.7566 (t70)
REVERT: B  277 SER cc_start: 0.8305 (p) cc_final: 0.7823 (m)
REVERT: G   20 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8105 (mtmt)
REVERT: R   48 CYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5447 (t)
REVERT: R   57 GLU cc_start: 0.7822 (tp30) cc_final: 0.7571 (tp30)
REVERT: R   61 VAL cc_start: 0.8433 (p) cc_final: 0.8155 (t)
REVERT: R   72 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7636 (mmm-85)
REVERT: R  118 MET cc_start: 0.8392 (ttm) cc_final: 0.8178 (ttm)
REVERT: R  209 MET cc_start: 0.8406 (tpp) cc_final: 0.7878 (mmm)
REVERT: R  249 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7928 (tt)
REVERT: R  281 LEU cc_start: 0.8306 (mt) cc_final: 0.8105 (mp)
  outliers start: 28
  outliers final: 19
  residues processed: 230
  average time/residue: 0.2987
  time to fit residues: 84.4577
Evaluate side-chains
  240 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain R residue   48 CYS
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  273 HIS
Chi-restraints excluded: chain R residue  291 MET
Chi-restraints excluded: chain R residue  300 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 16 optimal weight:    0.0980
   chunk 98 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 9 optimal weight:    0.2980
   chunk 66 optimal weight:    0.0270
   chunk 30 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.3638

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
N  53 GLN
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.131871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.115577 restraints weight = 11586.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.01
r_work: 0.3293 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3120
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3120 r_free = 0.3120    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3120
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.5014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8163  Z= 0.113
  Angle     :  0.510  10.199  11081  Z= 0.264
  Chirality :  0.039   0.128   1275
  Planarity :  0.003   0.035   1411
  Dihedral  :  4.102  20.529   1123
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.45 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.78 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.27), residues: 1021
  helix:  2.24 (0.25), residues: 401
  sheet:  0.23 (0.33), residues: 218
  loop : -0.16 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.011   0.001   PHE A 222 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  427)
  hydrogen bonds       : angle       4.33020 ( 1221)
  SS BOND              : bond        0.00181 (    3)
  SS BOND              : angle       0.37991 (    6)
  covalent geometry    : bond        0.00244 ( 8160)
  covalent geometry    : angle       0.51048 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 227
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6798 (mm-30)
REVERT: A  274 ASP cc_start: 0.8042 (t0) cc_final: 0.7748 (t0)
REVERT: A  292 ASN cc_start: 0.8577 (t0) cc_final: 0.8282 (t0)
REVERT: A  300 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7277 (mtpt)
REVERT: A  392 GLU cc_start: 0.6941 (pt0) cc_final: 0.6639 (pt0)
REVERT: B   13 GLN cc_start: 0.7874 (pp30) cc_final: 0.7592 (pp30)
REVERT: B   16 ASN cc_start: 0.8275 (m-40) cc_final: 0.7979 (m-40)
REVERT: B   23 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8298 (ttpt)
REVERT: B   59 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.8006 (t80)
REVERT: B   61 MET cc_start: 0.8343 (ppp) cc_final: 0.7810 (ppp)
REVERT: B   98 SER cc_start: 0.8548 (m) cc_final: 0.8252 (p)
REVERT: B  197 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7717 (tpt170)
REVERT: B  228 ASP cc_start: 0.7943 (m-30) cc_final: 0.7581 (m-30)
REVERT: B  230 ASN cc_start: 0.8285 (m-40) cc_final: 0.7915 (m-40)
REVERT: B  258 ASP cc_start: 0.8150 (t70) cc_final: 0.7500 (t70)
REVERT: B  277 SER cc_start: 0.8292 (p) cc_final: 0.7773 (m)
REVERT: B  289 TYR cc_start: 0.8701 (m-80) cc_final: 0.8198 (m-80)
REVERT: G   20 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7886 (mtmm)
REVERT: N  120 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8273 (mm-40)
REVERT: R   48 CYS cc_start: 0.5923 (OUTLIER) cc_final: 0.5494 (t)
REVERT: R   57 GLU cc_start: 0.7722 (tp30) cc_final: 0.7475 (tp30)
REVERT: R   61 VAL cc_start: 0.8367 (p) cc_final: 0.8089 (t)
REVERT: R   72 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7605 (mmm-85)
REVERT: R  137 SER cc_start: 0.8926 (t) cc_final: 0.8645 (p)
REVERT: R  209 MET cc_start: 0.8372 (tpp) cc_final: 0.7836 (mmm)
REVERT: R  249 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7924 (tt)
  outliers start: 21
  outliers final: 11
  residues processed: 236
  average time/residue: 0.2942
  time to fit residues: 85.7822
Evaluate side-chains
  235 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 220
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain R residue   48 CYS
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  291 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 96 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 95 optimal weight:    0.6980
   chunk 72 optimal weight:    0.4980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.126423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.110571 restraints weight = 11666.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.97
r_work: 0.3276 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3108
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3108 r_free = 0.3108    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3108
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8163  Z= 0.170
  Angle     :  0.556   9.838  11081  Z= 0.289
  Chirality :  0.041   0.165   1275
  Planarity :  0.004   0.038   1411
  Dihedral  :  4.236  20.195   1123
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.64 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 19.37 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.27), residues: 1021
  helix:  2.13 (0.25), residues: 404
  sheet:  0.15 (0.33), residues: 222
  loop : -0.10 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.012   0.002   PHE A 212 
 TYR   0.010   0.001   TYR B  59 
 ARG   0.004   0.001   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  427)
  hydrogen bonds       : angle       4.45470 ( 1221)
  SS BOND              : bond        0.00241 (    3)
  SS BOND              : angle       1.88285 (    6)
  covalent geometry    : bond        0.00380 ( 8160)
  covalent geometry    : angle       0.55419 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 210
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6913 (mm-30)
REVERT: A  220 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7616 (t-90)
REVERT: A  222 PHE cc_start: 0.8529 (m-80) cc_final: 0.8279 (m-80)
REVERT: A  274 ASP cc_start: 0.8049 (t0) cc_final: 0.7736 (t0)
REVERT: A  292 ASN cc_start: 0.8628 (t0) cc_final: 0.8378 (t0)
REVERT: A  300 LYS cc_start: 0.7686 (mtpt) cc_final: 0.7343 (mtpt)
REVERT: A  392 GLU cc_start: 0.7024 (pt0) cc_final: 0.6734 (pt0)
REVERT: B   13 GLN cc_start: 0.7873 (pp30) cc_final: 0.7572 (pp30)
REVERT: B   23 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8307 (ttpt)
REVERT: B   59 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.8057 (t80)
REVERT: B   61 MET cc_start: 0.8336 (ppp) cc_final: 0.7894 (ppp)
REVERT: B   87 THR cc_start: 0.8374 (m) cc_final: 0.8115 (t)
REVERT: B   98 SER cc_start: 0.8530 (m) cc_final: 0.8282 (p)
REVERT: B  101 MET cc_start: 0.8107 (mtp) cc_final: 0.7687 (mtp)
REVERT: B  197 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7624 (tpt170)
REVERT: B  230 ASN cc_start: 0.8346 (m-40) cc_final: 0.7952 (m-40)
REVERT: B  251 ARG cc_start: 0.8838 (mtt90) cc_final: 0.8533 (ttm170)
REVERT: B  258 ASP cc_start: 0.8118 (t70) cc_final: 0.7407 (t70)
REVERT: B  277 SER cc_start: 0.8293 (p) cc_final: 0.7801 (m)
REVERT: G   20 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7979 (mtmm)
REVERT: G   27 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8344 (mtt-85)
REVERT: N   86 LEU cc_start: 0.8701 (mt) cc_final: 0.8463 (mt)
REVERT: N  120 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8240 (mm-40)
REVERT: R   48 CYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5617 (t)
REVERT: R   57 GLU cc_start: 0.7798 (tp30) cc_final: 0.7571 (tp30)
REVERT: R   61 VAL cc_start: 0.8454 (p) cc_final: 0.8184 (t)
REVERT: R  120 PHE cc_start: 0.8600 (m-10) cc_final: 0.8389 (m-10)
REVERT: R  143 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8534 (p)
REVERT: R  209 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7867 (mmm)
REVERT: R  249 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8002 (tt)
  outliers start: 24
  outliers final: 16
  residues processed: 218
  average time/residue: 0.2845
  time to fit residues: 76.7688
Evaluate side-chains
  233 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLU
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain G residue   20 LYS
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue   48 CYS
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  291 MET
Chi-restraints excluded: chain R residue  300 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 63 optimal weight:    0.1980
   chunk 43 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0370
   chunk 9 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.4258

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

Flipped N/Q/H residues before XYZ refinement:
A 278 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.127600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.111582 restraints weight = 11761.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.99
r_work: 0.3290 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3124
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3124 r_free = 0.3124    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3124
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8163  Z= 0.122
  Angle     :  0.510   9.143  11081  Z= 0.267
  Chirality :  0.040   0.133   1275
  Planarity :  0.003   0.037   1411
  Dihedral  :  4.093  20.973   1123
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.06 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.60 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.30 (0.27), residues: 1021
  helix:  2.27 (0.25), residues: 401
  sheet:  0.13 (0.32), residues: 227
  loop : -0.11 (0.33), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.003   0.000   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  427)
  hydrogen bonds       : angle       4.32216 ( 1221)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       1.24780 (    6)
  covalent geometry    : bond        0.00268 ( 8160)
  covalent geometry    : angle       0.50966 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 209
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6878 (mm-30)
REVERT: A  220 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7603 (t-90)
REVERT: A  222 PHE cc_start: 0.8531 (m-80) cc_final: 0.8282 (m-80)
REVERT: A  274 ASP cc_start: 0.8046 (t0) cc_final: 0.7752 (t0)
REVERT: A  292 ASN cc_start: 0.8566 (t0) cc_final: 0.8278 (t0)
REVERT: A  300 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7345 (mtpt)
REVERT: A  347 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7623 (ttp80)
REVERT: A  392 GLU cc_start: 0.6959 (pt0) cc_final: 0.6663 (pt0)
REVERT: B   13 GLN cc_start: 0.7856 (pp30) cc_final: 0.7579 (pp30)
REVERT: B   16 ASN cc_start: 0.8290 (m-40) cc_final: 0.7965 (m-40)
REVERT: B   23 LYS cc_start: 0.8535 (ttpt) cc_final: 0.8308 (ttpt)
REVERT: B   59 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8041 (t80)
REVERT: B   61 MET cc_start: 0.8326 (ppp) cc_final: 0.7925 (ppp)
REVERT: B   87 THR cc_start: 0.8371 (m) cc_final: 0.8117 (t)
REVERT: B   98 SER cc_start: 0.8473 (m) cc_final: 0.8220 (p)
REVERT: B  197 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7613 (tpt170)
REVERT: B  230 ASN cc_start: 0.8323 (m-40) cc_final: 0.7945 (m-40)
REVERT: B  258 ASP cc_start: 0.8145 (t70) cc_final: 0.7494 (t70)
REVERT: B  277 SER cc_start: 0.8300 (p) cc_final: 0.7789 (m)
REVERT: B  289 TYR cc_start: 0.8712 (m-80) cc_final: 0.8237 (m-80)
REVERT: G   20 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7887 (mtmm)
REVERT: N  120 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8249 (mm-40)
REVERT: R   48 CYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5563 (t)
REVERT: R   57 GLU cc_start: 0.7744 (tp30) cc_final: 0.7485 (tp30)
REVERT: R   61 VAL cc_start: 0.8367 (p) cc_final: 0.8088 (t)
REVERT: R  209 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7857 (mmm)
REVERT: R  249 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7951 (tt)
  outliers start: 21
  outliers final: 13
  residues processed: 217
  average time/residue: 0.2748
  time to fit residues: 74.5280
Evaluate side-chains
  232 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 212
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue   48 CYS
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  291 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 93 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 278 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.112402 restraints weight = 11522.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 2.10
r_work: 0.3246 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.5321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8163  Z= 0.214
  Angle     :  0.577  10.024  11081  Z= 0.301
  Chirality :  0.042   0.141   1275
  Planarity :  0.004   0.041   1411
  Dihedral  :  4.354  21.436   1123
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.74 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.60 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: 1021
  helix:  2.20 (0.25), residues: 396
  sheet:  0.06 (0.33), residues: 224
  loop : -0.15 (0.33), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.017   0.002   PHE A 376 
 TYR   0.015   0.002   TYR B  59 
 ARG   0.003   0.001   ARG B 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04278 (  427)
  hydrogen bonds       : angle       4.56386 ( 1221)
  SS BOND              : bond        0.00317 (    3)
  SS BOND              : angle       1.36276 (    6)
  covalent geometry    : bond        0.00480 ( 8160)
  covalent geometry    : angle       0.57632 (11075)

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

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

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2042 Ramachandran restraints generated.
    1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 212
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6985 (mm-30)
REVERT: A  220 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7635 (t-90)
REVERT: A  222 PHE cc_start: 0.8558 (m-80) cc_final: 0.8333 (m-80)
REVERT: A  248 VAL cc_start: 0.8369 (t) cc_final: 0.8136 (m)
REVERT: A  274 ASP cc_start: 0.8082 (t0) cc_final: 0.7752 (t0)
REVERT: A  292 ASN cc_start: 0.8640 (t0) cc_final: 0.8370 (t0)
REVERT: A  300 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7361 (mtpt)
REVERT: A  347 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7597 (ttp80)
REVERT: A  392 GLU cc_start: 0.7095 (pt0) cc_final: 0.6788 (pt0)
REVERT: B   13 GLN cc_start: 0.7854 (pp30) cc_final: 0.7550 (pp30)
REVERT: B   23 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8403 (ttpt)
REVERT: B   59 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.8081 (t80)
REVERT: B   61 MET cc_start: 0.8349 (ppp) cc_final: 0.7950 (ppp)
REVERT: B   87 THR cc_start: 0.8405 (m) cc_final: 0.8131 (t)
REVERT: B   98 SER cc_start: 0.8563 (m) cc_final: 0.8287 (p)
REVERT: B  197 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7598 (tpt170)
REVERT: B  230 ASN cc_start: 0.8359 (m-40) cc_final: 0.7977 (m-40)
REVERT: B  251 ARG cc_start: 0.8869 (mtt90) cc_final: 0.8569 (ttm170)
REVERT: B  258 ASP cc_start: 0.8163 (t70) cc_final: 0.7467 (t70)
REVERT: B  277 SER cc_start: 0.8317 (p) cc_final: 0.7819 (m)
REVERT: G   20 LYS cc_start: 0.8454 (mtmt) cc_final: 0.8144 (mtmt)
REVERT: G   21 MET cc_start: 0.8471 (tpt) cc_final: 0.8219 (tpt)
REVERT: N  120 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8243 (mm-40)
REVERT: R   48 CYS cc_start: 0.5432 (OUTLIER) cc_final: 0.5195 (t)
REVERT: R   57 GLU cc_start: 0.7821 (tp30) cc_final: 0.7601 (tp30)
REVERT: R  143 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8465 (p)
REVERT: R  209 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7958 (mmm)
REVERT: R  249 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8019 (tt)
  outliers start: 23
  outliers final: 13
  residues processed: 220
  average time/residue: 0.2846
  time to fit residues: 77.6948
Evaluate side-chains
  229 residues out of total 871 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 208
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  347 ARG
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain B residue    6 GLN
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain N residue   11 LEU
Chi-restraints excluded: chain N residue   28 THR
Chi-restraints excluded: chain N residue   81 LEU
Chi-restraints excluded: chain R residue   48 CYS
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  209 MET
Chi-restraints excluded: chain R residue  249 LEU
Chi-restraints excluded: chain R residue  291 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 60 optimal weight:    0.1980
   chunk 52 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0470
   chunk 85 optimal weight:    0.6980
   chunk 59 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
A 220 HIS
A 278 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.112529 restraints weight = 11654.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.08
r_work: 0.3271 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8163  Z= 0.124
  Angle     :  0.534  10.229  11081  Z= 0.274
  Chirality :  0.040   0.131   1275
  Planarity :  0.003   0.038   1411
  Dihedral  :  4.153  21.550   1123
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.25 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.72 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.26 (0.27), residues: 1021
  helix:  2.25 (0.25), residues: 402
  sheet:  0.18 (0.33), residues: 216
  loop : -0.18 (0.33), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.011   0.001   PHE R 120 
 TYR   0.009   0.001   TYR B  59 
 ARG   0.007   0.000   ARG A 374 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  427)
  hydrogen bonds       : angle       4.36541 ( 1221)
  SS BOND              : bond        0.00229 (    3)
  SS BOND              : angle       0.93795 (    6)
  covalent geometry    : bond        0.00273 ( 8160)
  covalent geometry    : angle       0.53367 (11075)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4651.28 seconds
wall clock time: 81 minutes 3.47 seconds (4863.47 seconds total)