Starting phenix.real_space_refine
on Mon May 12 00:42:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j23_35943/05_2025/8j23_35943.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j23_35943/05_2025/8j23_35943.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j23_35943/05_2025/8j23_35943.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j23_35943/05_2025/8j23_35943.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j23_35943/05_2025/8j23_35943.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j23_35943/05_2025/8j23_35943.cif"
  }
  resolution = 3.2
  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=   0.021
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    5494      2.51       5
     N    1460      2.21       5
     O    1585      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 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: 8596
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2084
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 14, 'TRANS': 243}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1698
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 2, 'TRANS': 213}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 23
    Chain: "C"
      Number of atoms: 2610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2610
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "D"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 433
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "F"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
  Time building chain proxies: 4.98, per 1000 atoms: 0.58
  Number of scatterers: 8596
  At special positions: 0
  Unit cell: (117.52, 109.2, 123.76, 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    1585      8.00
     N    1460      7.00
     C    5494      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2054

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 14 sheets defined
      37.6% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 38
      removed outlier: 3.538A  pdb=" N   TYR A  14 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
      Proline residue:  A  23  - end of helix
      removed outlier: 3.527A  pdb=" N   GLY A  34 " --> pdb=" O   ARG A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 61
      removed outlier: 3.600A  pdb=" N   ILE A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 71
      removed outlier: 3.913A  pdb=" N   LYS A  65 " --> pdb=" O   LEU A  61 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE A  67 " --> pdb=" O   PRO A  63 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLU A  68 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 110
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.744A  pdb=" N   LEU A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 148
      removed outlier: 3.791A  pdb=" N   GLY A 126 " --> pdb=" O   ARG A 122 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   VAL A 144 " --> pdb=" O   HIS A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 204
      Proline residue:  A 177  - end of helix
      removed outlier: 3.746A  pdb=" N   ILE A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      Proline residue:  A 190  - end of helix
      removed outlier: 3.726A  pdb=" N   ARG A 200 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 247
      removed outlier: 3.581A  pdb=" N   ARG A 217 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   ARG A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      Proline residue:  A 236  - end of helix
      removed outlier: 3.840A  pdb=" N   HIS A 241 " --> pdb=" O   TYR A 237 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU A 242 " --> pdb=" O   ASN A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 274
      removed outlier: 3.663A  pdb=" N   VAL A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      Proline residue:  A 269  - end of helix
      removed outlier: 3.623A  pdb=" N   PHE A 272 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   PHE A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 32
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.709A  pdb=" N   ILE B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 4.287A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   HIS B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
    Processing helix  chain 'B' and resid 256 through 260
    Processing helix  chain 'B' and resid 270 through 279
      removed outlier: 3.749A  pdb=" N   GLU B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LYS B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
      removed outlier: 3.786A  pdb=" N   ILE B 285 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 309
    Processing helix  chain 'B' and resid 330 through 350
      removed outlier: 3.691A  pdb=" N   ASP B 341 " --> pdb=" O   ASP B 337 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL B 342 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ASP B 350 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 24
    Processing helix  chain 'C' and resid 27 through 32
    Processing helix  chain 'D' and resid 2 through 20
    Processing helix  chain 'D' and resid 25 through 40
    Processing helix  chain 'F' and resid 28 through 32
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 4.000A  pdb=" N   THR F  91 " --> pdb=" O   SER F  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190
      removed outlier: 9.231A  pdb=" N   ALA B 220 " --> pdb=" O   GLU B  33 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LYS B  35 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   ILE B 222 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 7.452A  pdb=" N   CYS B 224 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   PHE B 267 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   PHE B 223 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ASN B 269 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL B 225 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 44 through 49
      removed outlier: 5.872A  pdb=" N   THR C  45 " --> pdb=" O   ASN C 338 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ASN C 338 " --> pdb=" O   THR C  45 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG C  47 " --> pdb=" O   ILE C 336 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU C 334 " --> pdb=" O   LEU C  49 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 61
      removed outlier: 3.544A  pdb=" N   ALA C  58 " --> pdb=" O   ALA C  71 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER C  72 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LYS C  76 " --> pdb=" O   SER C  72 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ASP C  81 " --> pdb=" O   LYS C  87 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LYS C  87 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 98 through 103
      removed outlier: 7.029A  pdb=" N   GLY C 113 " --> pdb=" O   MET C  99 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   CYS C 101 " --> pdb=" O   ALA C 111 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   ALA C 111 " --> pdb=" O   CYS C 101 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   TYR C 103 " --> pdb=" O   TYR C 109 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   TYR C 109 " --> pdb=" O   TYR C 103 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   CYS C 119 " --> pdb=" O   GLU C 136 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   GLU C 136 " --> pdb=" O   CYS C 119 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   ILE C 121 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 144 through 149
      removed outlier: 3.719A  pdb=" N   THR C 176 " --> pdb=" O   LEU C 166 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   ASP C 168 " --> pdb=" O   GLN C 174 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   GLN C 174 " --> pdb=" O   ASP C 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 185 through 190
      removed outlier: 3.588A  pdb=" N   PHE C 197 " --> pdb=" O   TRP C 209 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   SER C 205 " --> pdb=" O   ALA C 201 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLN C 218 " --> pdb=" O   LEU C 208 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   ASP C 210 " --> pdb=" O   CYS C 216 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   CYS C 216 " --> pdb=" O   ASP C 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 232
      removed outlier: 3.620A  pdb=" N   LEU C 250 " --> pdb=" O   MET C 260 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   MET C 260 " --> pdb=" O   LEU C 250 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ASP C 252 " --> pdb=" O   GLU C 258 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLU C 258 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273
      removed outlier: 3.833A  pdb=" N   SER C 273 " --> pdb=" O   GLY C 286 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   ASN C 291 " --> pdb=" O   TYR C 287 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLY C 304 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   ASP C 296 " --> pdb=" O   ARG C 302 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   ARG C 302 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 11
      removed outlier: 3.585A  pdb=" N   THR F 115 " --> pdb=" O   TYR F  94 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR F  94 " --> pdb=" O   THR F 115 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   MET F  34 " --> pdb=" O   TYR F  50 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   TYR F  50 " --> pdb=" O   MET F  34 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   TRP F  36 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR F  50 " --> pdb=" O   TYR F  59 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11
      removed outlier: 3.585A  pdb=" N   THR F 115 " --> pdb=" O   TYR F  94 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR F  94 " --> pdb=" O   THR F 115 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG F  98 " --> pdb=" O   PHE F 110 " (cutoff:3.500A)
      removed outlier: 4.506A  pdb=" N   PHE F 110 " --> pdb=" O   ARG F  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 132 through 135
    Processing sheet with id=AB4, first strand: chain 'F' and resid 142 through 146
    Processing sheet with id=AB5, first strand: chain 'F' and resid 180 through 181
      removed outlier: 6.520A  pdb=" N   TRP F 162 " --> pdb=" O   LEU F 174 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   TYR F 176 " --> pdb=" O   LEU F 160 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU F 160 " --> pdb=" O   TYR F 176 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1182 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: 2.67

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2763
        1.34 -     1.46: 2144
        1.46 -     1.58: 3797
        1.58 -     1.70: 0
        1.70 -     1.81: 81
  Bond restraints: 8785
  Sorted by residual:
  bond pdb=" CB  PRO A 123 "
       pdb=" CG  PRO A 123 "
    ideal  model  delta    sigma   weight residual
    1.492  1.569 -0.077 5.00e-02 4.00e+02 2.38e+00
  bond pdb=" CA  TYR F 221 "
       pdb=" C   TYR F 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.541 -0.017 1.26e-02 6.30e+03 1.89e+00
  bond pdb=" CG  PRO A 123 "
       pdb=" CD  PRO A 123 "
    ideal  model  delta    sigma   weight residual
    1.503  1.547 -0.044 3.40e-02 8.65e+02 1.69e+00
  bond pdb=" CB  PRO F 222 "
       pdb=" CG  PRO F 222 "
    ideal  model  delta    sigma   weight residual
    1.492  1.557 -0.065 5.00e-02 4.00e+02 1.66e+00
  bond pdb=" CB  ASN C 235 "
       pdb=" CG  ASN C 235 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 2.50e-02 1.60e+03 1.52e+00
  ... (remaining 8780 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.40: 11889
        4.40 -     8.81: 18
        8.81 -    13.21: 4
       13.21 -    17.62: 0
       17.62 -    22.02: 1
  Bond angle restraints: 11912
  Sorted by residual:
  angle pdb=" N   TYR F 221 "
        pdb=" CA  TYR F 221 "
        pdb=" C   TYR F 221 "
      ideal   model   delta    sigma   weight residual
     109.81  131.83  -22.02 2.21e+00 2.05e-01 9.93e+01
  angle pdb=" C   TYR F 221 "
        pdb=" N   PRO F 222 "
        pdb=" CA  PRO F 222 "
      ideal   model   delta    sigma   weight residual
     119.84  132.25  -12.41 1.25e+00 6.40e-01 9.85e+01
  angle pdb=" C   PRO F 222 "
        pdb=" CA  PRO F 222 "
        pdb=" CB  PRO F 222 "
      ideal   model   delta    sigma   weight residual
     111.56  124.71  -13.15 1.65e+00 3.67e-01 6.35e+01
  angle pdb=" CA  PRO F 222 "
        pdb=" N   PRO F 222 "
        pdb=" CD  PRO F 222 "
      ideal   model   delta    sigma   weight residual
     112.00  106.05    5.95 1.40e+00 5.10e-01 1.80e+01
  angle pdb=" C   GLU F 220 "
        pdb=" N   TYR F 221 "
        pdb=" CA  TYR F 221 "
      ideal   model   delta    sigma   weight residual
     121.80  130.60   -8.80 2.44e+00 1.68e-01 1.30e+01
  ... (remaining 11907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.81: 4690
       24.81 -    49.62: 453
       49.62 -    74.43: 31
       74.43 -    99.25: 7
       99.25 -   124.06: 1
  Dihedral angle restraints: 5182
    sinusoidal: 1995
      harmonic: 3187
  Sorted by residual:
  dihedral pdb=" CA  TYR F 221 "
           pdb=" C   TYR F 221 "
           pdb=" N   PRO F 222 "
           pdb=" CA  PRO F 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   55.94  124.06     0      5.00e+00 4.00e-02 6.16e+02
  dihedral pdb=" N   TYR F 221 "
           pdb=" C   TYR F 221 "
           pdb=" CA  TYR F 221 "
           pdb=" CB  TYR F 221 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  158.56  -35.76     0      2.50e+00 1.60e-01 2.05e+02
  dihedral pdb=" C   TYR F 221 "
           pdb=" N   TYR F 221 "
           pdb=" CA  TYR F 221 "
           pdb=" CB  TYR F 221 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -158.33   35.73     0      2.50e+00 1.60e-01 2.04e+02
  ... (remaining 5179 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.326: 1347
       0.326 -    0.653: 0
       0.653 -    0.979: 1
       0.979 -    1.306: 0
       1.306 -    1.632: 1
  Chirality restraints: 1349
  Sorted by residual:
  chirality pdb=" CA  TYR F 221 "
            pdb=" N   TYR F 221 "
            pdb=" C   TYR F 221 "
            pdb=" CB  TYR F 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.88    1.63 2.00e-01 2.50e+01 6.66e+01
  chirality pdb=" CA  PRO F 222 "
            pdb=" N   PRO F 222 "
            pdb=" C   PRO F 222 "
            pdb=" CB  PRO F 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.94    0.77 2.00e-01 2.50e+01 1.50e+01
  chirality pdb=" CA  ILE F 100 "
            pdb=" N   ILE F 100 "
            pdb=" C   ILE F 100 "
            pdb=" CB  ILE F 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 1346 not shown)

  Planarity restraints: 1504
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 122 "   -0.077 5.00e-02 4.00e+02   1.15e-01 2.10e+01
        pdb=" N   PRO A 123 "    0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO A 123 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A 123 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 233 "   -0.068 5.00e-02 4.00e+02   1.01e-01 1.64e+01
        pdb=" N   PRO C 234 "    0.175 5.00e-02 4.00e+02
        pdb=" CA  PRO C 234 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO C 234 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR F 221 "   -0.062 5.00e-02 4.00e+02   9.14e-02 1.34e+01
        pdb=" N   PRO F 222 "    0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO F 222 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO F 222 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 1501 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 150
        2.67 -     3.23: 7875
        3.23 -     3.79: 13577
        3.79 -     4.34: 18090
        4.34 -     4.90: 30431
  Nonbonded interactions: 70123
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  84 "
            pdb=" OD1 ASN C  86 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" O   ILE C  56 "
            pdb=" OG  SER C 314 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OG  SER C 106 "
            pdb=" OD1 ASN C 108 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG  SER C 159 "
            pdb=" OD1 ASP C 161 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG1 THR C  63 "
            pdb=" O   PRO C 105 "
     model   vdw
     2.265 3.040
  ... (remaining 70118 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=0.02 max=1.00 mean=0.99
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:             3.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.610
  Find NCS groups from input model:        0.120
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
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      :  0.002   0.077   8786  Z= 0.095
  Angle     :  0.570  22.025  11914  Z= 0.295
  Chirality :  0.062   1.632   1349
  Planarity :  0.006   0.115   1504
  Dihedral  : 17.342 124.058   3125
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.32 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  : 30.60 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.09 %

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:  0.73 (0.26), residues: 1083
  helix:  1.42 (0.27), residues: 375
  sheet:  0.86 (0.33), residues: 259
  loop : -0.50 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  75 
 HIS   0.002   0.000   HIS F  35 
 PHE   0.028   0.001   PHE B 334 
 TYR   0.044   0.001   TYR F 221 
 ARG   0.004   0.000   ARG D  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25826 (  416)
  hydrogen bonds       : angle       7.90055 ( 1182)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.49406 (    2)
  covalent geometry    : bond        0.00233 ( 8785)
  covalent geometry    : angle       0.57000 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 215
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  193 VAL cc_start: 0.8069 (m) cc_final: 0.7806 (p)
REVERT: A  249 LYS cc_start: 0.6306 (OUTLIER) cc_final: 0.5969 (tptm)
REVERT: B  197 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7400 (mttp)
REVERT: B  209 LYS cc_start: 0.7441 (ptmt) cc_final: 0.7174 (ptpp)
REVERT: D   17 MET cc_start: 0.6721 (mmp) cc_final: 0.6513 (mmp)
REVERT: F   39 GLN cc_start: 0.7687 (tt0) cc_final: 0.7451 (tt0)
REVERT: F  126 MET cc_start: 0.7862 (tpp) cc_final: 0.7352 (tpp)
  outliers start: 4
  outliers final: 1
  residues processed: 216
  average time/residue: 0.2286
  time to fit residues: 65.7423
Evaluate side-chains
  205 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 203
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 LYS
Chi-restraints excluded: chain B residue  187 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0040
   chunk 51 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.7396

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
A 264 ASN
** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 108 ASN
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 338 ASN
F 180 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.148242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.130321 restraints weight = 12015.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3600 rms_B_bonded: 2.12
r_work: 0.3483 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3306 r_free = 0.3306    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
r_final: 0.3306
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8786  Z= 0.192
  Angle     :  0.622  14.197  11914  Z= 0.325
  Chirality :  0.045   0.318   1349
  Planarity :  0.006   0.076   1504
  Dihedral  :  4.319  40.777   1195
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.88 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 25.00 %
    Favored  : 69.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.09 %

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:  0.88 (0.26), residues: 1083
  helix:  1.55 (0.27), residues: 391
  sheet:  0.82 (0.33), residues: 258
  loop : -0.40 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  75 
 HIS   0.005   0.001   HIS C  89 
 PHE   0.021   0.002   PHE B 259 
 TYR   0.019   0.002   TYR F  59 
 ARG   0.008   0.001   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04789 (  416)
  hydrogen bonds       : angle       5.06159 ( 1182)
  SS BOND              : bond        0.00817 (    1)
  SS BOND              : angle       0.93859 (    2)
  covalent geometry    : bond        0.00438 ( 8785)
  covalent geometry    : angle       0.62220 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 223
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  119 LEU cc_start: 0.7078 (pt) cc_final: 0.6643 (pp)
REVERT: A  184 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6203 (tt)
REVERT: A  186 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7223 (tp)
REVERT: A  267 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7226 (tt)
REVERT: A  270 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7285 (tt)
REVERT: A  273 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.4258 (p90)
REVERT: B   46 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6355 (mttp)
REVERT: B  197 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7683 (mtpp)
REVERT: B  209 LYS cc_start: 0.7913 (ptmt) cc_final: 0.7710 (ptmt)
REVERT: B  259 PHE cc_start: 0.8166 (m-10) cc_final: 0.7611 (m-80)
REVERT: B  312 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7514 (mttp)
REVERT: C   23 CYS cc_start: 0.7843 (m) cc_final: 0.7441 (m)
REVERT: C   47 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7034 (mpt180)
REVERT: C   66 ARG cc_start: 0.6713 (ttp-170) cc_final: 0.5962 (ttp80)
REVERT: F   39 GLN cc_start: 0.8132 (tt0) cc_final: 0.7873 (tt0)
  outliers start: 53
  outliers final: 23
  residues processed: 245
  average time/residue: 0.2220
  time to fit residues: 73.0020
Evaluate side-chains
  245 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 215
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  186 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  215 MET
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  272 THR
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue  115 THR
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0770
   chunk 4 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 238 ASN
B 213 HIS
** C 117 ASN ** 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 = 0.3796 r_free = 0.3796 target = 0.139272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.121337 restraints weight = 12188.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.10
r_work: 0.3444 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8786  Z= 0.156
  Angle     :  0.571  10.751  11914  Z= 0.292
  Chirality :  0.044   0.312   1349
  Planarity :  0.005   0.069   1504
  Dihedral  :  4.203  31.316   1191
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.79 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 24.68 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    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:  0.88 (0.26), residues: 1083
  helix:  1.65 (0.27), residues: 395
  sheet:  0.61 (0.32), residues: 269
  loop : -0.40 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  75 
 HIS   0.003   0.001   HIS C  89 
 PHE   0.016   0.002   PHE C 197 
 TYR   0.016   0.001   TYR F  59 
 ARG   0.005   0.000   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04136 (  416)
  hydrogen bonds       : angle       4.64705 ( 1182)
  SS BOND              : bond        0.00646 (    1)
  SS BOND              : angle       1.00199 (    2)
  covalent geometry    : bond        0.00354 ( 8785)
  covalent geometry    : angle       0.57086 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 212
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6196 (tt)
REVERT: A  270 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7577 (tt)
REVERT: A  273 TYR cc_start: 0.5047 (OUTLIER) cc_final: 0.4236 (p90)
REVERT: B  197 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7488 (mtpp)
REVERT: B  209 LYS cc_start: 0.8017 (ptmt) cc_final: 0.7804 (ptmt)
REVERT: B  298 GLU cc_start: 0.6118 (pt0) cc_final: 0.5839 (pt0)
REVERT: B  312 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7658 (mttp)
REVERT: C   23 CYS cc_start: 0.7786 (m) cc_final: 0.7322 (m)
REVERT: C   35 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7611 (tp)
REVERT: C   43 MET cc_start: 0.8107 (mtp) cc_final: 0.7898 (mtt)
REVERT: C   47 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7213 (mpt180)
REVERT: C  168 ASP cc_start: 0.6944 (t0) cc_final: 0.6703 (t0)
REVERT: C  208 LEU cc_start: 0.7864 (tp) cc_final: 0.7660 (tp)
REVERT: C  264 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8574 (t-90)
  outliers start: 47
  outliers final: 26
  residues processed: 233
  average time/residue: 0.2149
  time to fit residues: 67.8782
Evaluate side-chains
  242 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain C residue   35 ILE
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  264 HIS
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  177 ARG
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 101 optimal weight:    0.1980
   chunk 29 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 244 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.139927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.122571 restraints weight = 12053.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.05
r_work: 0.3455 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3293
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3293 r_free = 0.3293    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       28 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3292 r_free = 0.3292    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3292
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8786  Z= 0.148
  Angle     :  0.557   9.730  11914  Z= 0.283
  Chirality :  0.043   0.311   1349
  Planarity :  0.005   0.103   1504
  Dihedral  :  4.129  29.039   1190
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.32 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 24.35 %
    Favored  : 70.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1083
  helix:  1.75 (0.27), residues: 397
  sheet:  0.51 (0.32), residues: 270
  loop : -0.45 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  75 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.016   0.002   PHE C 197 
 TYR   0.014   0.001   TYR F  59 
 ARG   0.007   0.000   ARG B  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03695 (  416)
  hydrogen bonds       : angle       4.48410 ( 1182)
  SS BOND              : bond        0.00797 (    1)
  SS BOND              : angle       1.52612 (    2)
  covalent geometry    : bond        0.00343 ( 8785)
  covalent geometry    : angle       0.55627 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 218
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7154 (mm) cc_final: 0.6901 (mp)
REVERT: A  184 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6189 (tt)
REVERT: A  273 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4315 (p90)
REVERT: B   46 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6385 (mttm)
REVERT: B  197 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7393 (mtpp)
REVERT: B  209 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7751 (ptmt)
REVERT: B  298 GLU cc_start: 0.6161 (pt0) cc_final: 0.5895 (pt0)
REVERT: B  312 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7646 (mttp)
REVERT: C   23 CYS cc_start: 0.7806 (m) cc_final: 0.7345 (m)
REVERT: C   35 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7636 (tp)
REVERT: C   43 MET cc_start: 0.8193 (mtp) cc_final: 0.7981 (mtt)
REVERT: C   47 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7109 (mpt180)
REVERT: C  168 ASP cc_start: 0.6930 (t0) cc_final: 0.6681 (t0)
REVERT: C  217 ARG cc_start: 0.8124 (mtt90) cc_final: 0.7781 (mtt90)
REVERT: C  226 ASP cc_start: 0.7932 (p0) cc_final: 0.7505 (p0)
REVERT: F  141 VAL cc_start: 0.7599 (p) cc_final: 0.7395 (m)
  outliers start: 51
  outliers final: 31
  residues processed: 248
  average time/residue: 0.2195
  time to fit residues: 72.9365
Evaluate side-chains
  255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 219
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain C residue   35 ILE
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  177 ARG
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 100 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   chunk 90 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.138032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.120676 restraints weight = 12069.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.05
r_work: 0.3440 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3269 r_free = 0.3269    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8786  Z= 0.156
  Angle     :  0.568  11.581  11914  Z= 0.287
  Chirality :  0.043   0.285   1349
  Planarity :  0.005   0.100   1504
  Dihedral  :  4.203  24.806   1190
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.88 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 23.81 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.26), residues: 1083
  helix:  1.73 (0.27), residues: 402
  sheet:  0.49 (0.31), residues: 268
  loop : -0.52 (0.30), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  75 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.017   0.002   PHE C 197 
 TYR   0.014   0.001   TYR F  59 
 ARG   0.006   0.000   ARG D  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  416)
  hydrogen bonds       : angle       4.44752 ( 1182)
  SS BOND              : bond        0.00779 (    1)
  SS BOND              : angle       1.37609 (    2)
  covalent geometry    : bond        0.00363 ( 8785)
  covalent geometry    : angle       0.56794 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 214
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: A  184 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6177 (tt)
REVERT: A  273 TYR cc_start: 0.5201 (OUTLIER) cc_final: 0.4318 (p90)
REVERT: B   46 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6264 (mttm)
REVERT: B  197 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7421 (mtpp)
REVERT: B  209 LYS cc_start: 0.8026 (ptmt) cc_final: 0.7803 (ptmt)
REVERT: B  243 MET cc_start: 0.8348 (tpp) cc_final: 0.8103 (tpp)
REVERT: B  298 GLU cc_start: 0.6350 (pt0) cc_final: 0.6035 (pt0)
REVERT: B  312 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7630 (mttm)
REVERT: C   23 CYS cc_start: 0.7814 (m) cc_final: 0.7351 (m)
REVERT: C   35 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7657 (tp)
REVERT: C   47 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7068 (mpt180)
REVERT: C  208 LEU cc_start: 0.7872 (tp) cc_final: 0.7659 (tp)
REVERT: C  211 VAL cc_start: 0.7932 (t) cc_final: 0.7685 (m)
REVERT: C  217 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7509 (mtt90)
REVERT: C  226 ASP cc_start: 0.7923 (p0) cc_final: 0.7505 (p0)
REVERT: C  264 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8588 (t-90)
REVERT: F  141 VAL cc_start: 0.7590 (p) cc_final: 0.7387 (m)
  outliers start: 55
  outliers final: 41
  residues processed: 250
  average time/residue: 0.2241
  time to fit residues: 75.0450
Evaluate side-chains
  263 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 216
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  254 ARG
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   35 ILE
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  264 HIS
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  276 PHE
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  177 ARG
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 1 optimal weight:    0.3980
   chunk 92 optimal weight:    0.4980
   chunk 65 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0980
   chunk 21 optimal weight:    0.5980
   chunk 48 optimal weight:    5.9990
   chunk 43 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 89 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
B 269 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.138604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.121255 restraints weight = 12033.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.06
r_work: 0.3453 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3296 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8786  Z= 0.119
  Angle     :  0.551  12.244  11914  Z= 0.278
  Chirality :  0.042   0.261   1349
  Planarity :  0.005   0.100   1504
  Dihedral  :  4.124  24.886   1190
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.23 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 25.32 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1083
  helix:  1.81 (0.27), residues: 403
  sheet:  0.43 (0.32), residues: 266
  loop : -0.47 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  75 
 HIS   0.003   0.001   HIS F  35 
 PHE   0.015   0.001   PHE C 197 
 TYR   0.011   0.001   TYR F 101 
 ARG   0.007   0.000   ARG A 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  416)
  hydrogen bonds       : angle       4.31059 ( 1182)
  SS BOND              : bond        0.00640 (    1)
  SS BOND              : angle       1.21094 (    2)
  covalent geometry    : bond        0.00273 ( 8785)
  covalent geometry    : angle       0.55065 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 215
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7069 (mm) cc_final: 0.6842 (mp)
REVERT: A  105 ILE cc_start: 0.8085 (mt) cc_final: 0.7702 (tt)
REVERT: A  184 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6138 (tt)
REVERT: A  273 TYR cc_start: 0.5132 (OUTLIER) cc_final: 0.4237 (p90)
REVERT: B   46 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6234 (mttm)
REVERT: B  192 LYS cc_start: 0.8837 (mttm) cc_final: 0.8487 (ttmm)
REVERT: B  197 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7378 (mtpp)
REVERT: B  209 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7759 (ptmt)
REVERT: B  298 GLU cc_start: 0.6310 (pt0) cc_final: 0.5981 (pt0)
REVERT: B  312 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7602 (mttm)
REVERT: C   23 CYS cc_start: 0.7776 (m) cc_final: 0.7317 (m)
REVERT: C   35 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7622 (tp)
REVERT: C   47 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7057 (mpt180)
REVERT: C  208 LEU cc_start: 0.7858 (tp) cc_final: 0.7611 (tp)
REVERT: C  217 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7712 (mtt90)
REVERT: C  226 ASP cc_start: 0.7949 (p0) cc_final: 0.7525 (p0)
REVERT: F  216 MET cc_start: 0.8103 (ttp) cc_final: 0.7791 (ttp)
  outliers start: 53
  outliers final: 36
  residues processed: 243
  average time/residue: 0.2251
  time to fit residues: 72.4627
Evaluate side-chains
  253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 212
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   29 LYS
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   35 ILE
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  202 CYS
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  276 PHE
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
B 204 GLN
F 218 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.136641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.119343 restraints weight = 12122.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.05
r_work: 0.3410 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8786  Z= 0.188
  Angle     :  0.599  12.979  11914  Z= 0.302
  Chirality :  0.044   0.279   1349
  Planarity :  0.005   0.098   1504
  Dihedral  :  4.350  24.529   1190
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.97 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 25.32 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1083
  helix:  1.70 (0.27), residues: 402
  sheet:  0.26 (0.31), residues: 272
  loop : -0.51 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  80 
 HIS   0.004   0.001   HIS C 140 
 PHE   0.019   0.002   PHE C 197 
 TYR   0.014   0.002   TYR F 101 
 ARG   0.007   0.001   ARG A 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03653 (  416)
  hydrogen bonds       : angle       4.43821 ( 1182)
  SS BOND              : bond        0.00952 (    1)
  SS BOND              : angle       1.46107 (    2)
  covalent geometry    : bond        0.00437 ( 8785)
  covalent geometry    : angle       0.59869 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 214
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7094 (mm) cc_final: 0.6862 (mp)
REVERT: A  184 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6226 (tt)
REVERT: A  273 TYR cc_start: 0.5342 (OUTLIER) cc_final: 0.4395 (p90)
REVERT: B   32 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7704 (ttm-80)
REVERT: B   46 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6486 (mttm)
REVERT: B  197 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7458 (mtpp)
REVERT: B  209 LYS cc_start: 0.8070 (ptmt) cc_final: 0.7836 (ptmt)
REVERT: B  298 GLU cc_start: 0.6449 (pt0) cc_final: 0.6113 (pt0)
REVERT: B  312 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7610 (mttm)
REVERT: C   23 CYS cc_start: 0.7814 (m) cc_final: 0.7336 (m)
REVERT: C   35 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7669 (tp)
REVERT: C   47 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7024 (mpt180)
REVERT: C  217 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7706 (mtt90)
REVERT: C  226 ASP cc_start: 0.7931 (p0) cc_final: 0.7449 (p0)
REVERT: C  298 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8235 (mt)
  outliers start: 55
  outliers final: 41
  residues processed: 246
  average time/residue: 0.2230
  time to fit residues: 73.2917
Evaluate side-chains
  259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 212
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   35 ILE
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  202 CYS
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain D residue   24 ILE
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 106 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 105 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0010
   chunk 59 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0870
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.4564

-------------------------------------------------------------------------------
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 = 0.3784 r_free = 0.3784 target = 0.138335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.120938 restraints weight = 12214.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3547 rms_B_bonded: 2.08
r_work: 0.3433 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8786  Z= 0.129
  Angle     :  0.568  12.965  11914  Z= 0.283
  Chirality :  0.042   0.255   1349
  Planarity :  0.005   0.097   1504
  Dihedral  :  4.227  25.285   1190
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.42 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 25.32 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1083
  helix:  1.79 (0.27), residues: 403
  sheet:  0.24 (0.31), residues: 272
  loop : -0.46 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  80 
 HIS   0.003   0.001   HIS F  35 
 PHE   0.017   0.001   PHE C 197 
 TYR   0.013   0.001   TYR F 101 
 ARG   0.007   0.000   ARG F 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03312 (  416)
  hydrogen bonds       : angle       4.28417 ( 1182)
  SS BOND              : bond        0.00680 (    1)
  SS BOND              : angle       1.15112 (    2)
  covalent geometry    : bond        0.00296 ( 8785)
  covalent geometry    : angle       0.56831 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 216
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7034 (mm) cc_final: 0.6798 (mp)
REVERT: A  105 ILE cc_start: 0.8111 (mt) cc_final: 0.7726 (tt)
REVERT: A  184 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6177 (tt)
REVERT: A  216 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7397 (ttm170)
REVERT: A  273 TYR cc_start: 0.5341 (OUTLIER) cc_final: 0.4417 (p90)
REVERT: B   32 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7655 (ttm-80)
REVERT: B   46 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6514 (mttm)
REVERT: B  197 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7379 (mtpp)
REVERT: B  209 LYS cc_start: 0.8032 (ptmt) cc_final: 0.7816 (ptmt)
REVERT: B  298 GLU cc_start: 0.6371 (pt0) cc_final: 0.6025 (pt0)
REVERT: B  312 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7602 (mttm)
REVERT: C   23 CYS cc_start: 0.7778 (m) cc_final: 0.7240 (m)
REVERT: C   35 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7626 (tp)
REVERT: C   47 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7022 (mpt180)
REVERT: C  217 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7729 (mtt90)
REVERT: C  226 ASP cc_start: 0.7932 (p0) cc_final: 0.7444 (p0)
REVERT: F   46 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7069 (pt0)
REVERT: F  189 PHE cc_start: 0.8370 (m-80) cc_final: 0.7943 (m-80)
  outliers start: 54
  outliers final: 40
  residues processed: 247
  average time/residue: 0.2353
  time to fit residues: 77.0995
Evaluate side-chains
  257 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 210
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue   62 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  216 ARG
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   35 ILE
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  202 CYS
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  276 PHE
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  146 ARG
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 56 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0670
   chunk 96 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0980
   chunk 98 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   overall best weight:    0.3918

-------------------------------------------------------------------------------
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 = 0.3786 r_free = 0.3786 target = 0.138419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.121053 restraints weight = 12158.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 2.07
r_work: 0.3441 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3281
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3281 r_free = 0.3281    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.3281
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8786  Z= 0.123
  Angle     :  0.572  12.896  11914  Z= 0.284
  Chirality :  0.042   0.246   1349
  Planarity :  0.005   0.096   1504
  Dihedral  :  4.160  24.975   1190
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.42 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.51 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1083
  helix:  1.82 (0.27), residues: 403
  sheet:  0.15 (0.31), residues: 271
  loop : -0.39 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  80 
 HIS   0.003   0.001   HIS F  35 
 PHE   0.015   0.001   PHE C 197 
 TYR   0.012   0.001   TYR F 101 
 ARG   0.006   0.000   ARG A 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03243 (  416)
  hydrogen bonds       : angle       4.24016 ( 1182)
  SS BOND              : bond        0.00667 (    1)
  SS BOND              : angle       1.09478 (    2)
  covalent geometry    : bond        0.00279 ( 8785)
  covalent geometry    : angle       0.57174 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 210
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7033 (mm) cc_final: 0.6789 (mp)
REVERT: A  105 ILE cc_start: 0.8070 (mt) cc_final: 0.7706 (tt)
REVERT: A  216 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7395 (ttm170)
REVERT: A  273 TYR cc_start: 0.5231 (OUTLIER) cc_final: 0.4327 (p90)
REVERT: B   32 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7582 (ttm-80)
REVERT: B   46 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6432 (mttm)
REVERT: B  197 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7392 (mtpp)
REVERT: B  209 LYS cc_start: 0.8020 (ptmt) cc_final: 0.7801 (ptmt)
REVERT: B  298 GLU cc_start: 0.6364 (pt0) cc_final: 0.6009 (pt0)
REVERT: B  312 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7610 (mttm)
REVERT: C   23 CYS cc_start: 0.7780 (m) cc_final: 0.7238 (m)
REVERT: C   35 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7584 (tp)
REVERT: C   47 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6919 (mpt180)
REVERT: C  211 VAL cc_start: 0.7969 (t) cc_final: 0.7732 (m)
REVERT: C  217 ARG cc_start: 0.8146 (mtt90) cc_final: 0.7716 (mtt90)
REVERT: C  226 ASP cc_start: 0.7910 (p0) cc_final: 0.7430 (p0)
REVERT: F   46 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7057 (pt0)
REVERT: F  189 PHE cc_start: 0.8361 (m-80) cc_final: 0.7940 (m-80)
  outliers start: 46
  outliers final: 35
  residues processed: 236
  average time/residue: 0.2406
  time to fit residues: 74.0991
Evaluate side-chains
  249 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 208
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  216 ARG
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  345 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   35 ILE
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  202 CYS
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  275 SER
Chi-restraints excluded: chain C residue  276 PHE
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain F residue   46 GLU
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  146 ARG
Chi-restraints excluded: chain F residue  177 ARG
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0470
   chunk 60 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    0.3980
   chunk 106 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0050
   chunk 39 optimal weight:    0.0270
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.2150

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.139998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.122428 restraints weight = 12161.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.12
r_work: 0.3463 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3307 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8786  Z= 0.102
  Angle     :  0.550  12.636  11914  Z= 0.273
  Chirality :  0.042   0.171   1349
  Planarity :  0.005   0.086   1504
  Dihedral  :  4.019  24.869   1190
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 27.91 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1083
  helix:  1.90 (0.27), residues: 400
  sheet:  0.30 (0.31), residues: 265
  loop : -0.38 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  75 
 HIS   0.003   0.001   HIS F  35 
 PHE   0.012   0.001   PHE C 197 
 TYR   0.014   0.001   TYR F 221 
 ARG   0.006   0.000   ARG A 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03009 (  416)
  hydrogen bonds       : angle       4.11455 ( 1182)
  SS BOND              : bond        0.00531 (    1)
  SS BOND              : angle       0.93666 (    2)
  covalent geometry    : bond        0.00228 ( 8785)
  covalent geometry    : angle       0.54995 (11912)

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 210
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.6989 (mm) cc_final: 0.6725 (mp)
REVERT: A  105 ILE cc_start: 0.8100 (mt) cc_final: 0.7743 (tt)
REVERT: A  216 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7269 (ttm170)
REVERT: A  273 TYR cc_start: 0.5235 (OUTLIER) cc_final: 0.4351 (p90)
REVERT: B   32 ARG cc_start: 0.7849 (ttm-80) cc_final: 0.7480 (ttm-80)
REVERT: B   46 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6326 (mttm)
REVERT: B  197 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7385 (mtpp)
REVERT: B  209 LYS cc_start: 0.7786 (ptmt) cc_final: 0.7584 (ptmt)
REVERT: B  298 GLU cc_start: 0.6316 (pt0) cc_final: 0.5941 (pt0)
REVERT: B  312 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7620 (mttm)
REVERT: C   23 CYS cc_start: 0.7816 (m) cc_final: 0.7332 (m)
REVERT: C   47 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7027 (mpt180)
REVERT: C  126 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8024 (t)
REVERT: C  217 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7752 (mtt90)
REVERT: C  226 ASP cc_start: 0.7938 (p0) cc_final: 0.7511 (p0)
REVERT: C  302 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.7403 (mtt180)
REVERT: F  189 PHE cc_start: 0.8363 (m-80) cc_final: 0.7936 (m-80)
REVERT: F  223 LEU cc_start: 0.7737 (mp) cc_final: 0.7482 (mt)
  outliers start: 35
  outliers final: 28
  residues processed: 229
  average time/residue: 0.2390
  time to fit residues: 72.4261
Evaluate side-chains
  240 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 207
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue  216 ARG
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   46 LYS
Chi-restraints excluded: chain B residue   48 THR
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  126 THR
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  169 ILE
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  210 ASP
Chi-restraints excluded: chain C residue  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  268 ILE
Chi-restraints excluded: chain C residue  276 PHE
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  329 SER
Chi-restraints excluded: chain D residue   47 LEU
Chi-restraints excluded: chain F residue   63 THR
Chi-restraints excluded: chain F residue   93 MET
Chi-restraints excluded: chain F residue  146 ARG
Chi-restraints excluded: chain F residue  177 ARG
Chi-restraints excluded: chain F residue  185 VAL
Chi-restraints excluded: chain F residue  201 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.1980
   chunk 99 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 98 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 228 ASN
** F  39 GLN ** 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 = 0.3771 r_free = 0.3771 target = 0.137376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119938 restraints weight = 12068.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.06
r_work: 0.3411 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3212
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3212 r_free = 0.3212    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3212
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.3706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8786  Z= 0.172
  Angle     :  0.596  12.981  11914  Z= 0.299
  Chirality :  0.044   0.194   1349
  Planarity :  0.005   0.092   1504
  Dihedral  :  4.280  24.424   1190
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 27.59 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1083
  helix:  1.82 (0.27), residues: 402
  sheet:  0.20 (0.31), residues: 269
  loop : -0.43 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F  47 
 HIS   0.007   0.001   HIS B 188 
 PHE   0.018   0.002   PHE C 197 
 TYR   0.018   0.002   TYR F 213 
 ARG   0.007   0.000   ARG F 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03503 (  416)
  hydrogen bonds       : angle       4.33241 ( 1182)
  SS BOND              : bond        0.00892 (    1)
  SS BOND              : angle       1.42961 (    2)
  covalent geometry    : bond        0.00401 ( 8785)
  covalent geometry    : angle       0.59590 (11912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5264.66 seconds
wall clock time: 91 minutes 41.76 seconds (5501.76 seconds total)