Starting phenix.real_space_refine
on Fri Aug 22 23:32:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j23_35943/08_2025/8j23_35943.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j23_35943/08_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_35943/08_2025/8j23_35943.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j23_35943/08_2025/8j23_35943.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j23_35943/08_2025/8j23_35943.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j23_35943/08_2025/8j23_35943.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 3}
          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: 2.26, per 1000 atoms: 0.26
  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: 0.69
  Conformation dependent library (CDL) restraints added in 468.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.35
  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: 1.33

  Time building geometry restraints manager: 0.95 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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.540
  Find NCS groups from input model:        0.040
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.660
-------------------------------------------------------------------------------
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 : 7.84
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG D  23 
 TYR   0.044   0.001   TYR F 221 
 PHE   0.028   0.001   PHE B 334 
 TRP   0.020   0.001   TRP A  75 
 HIS   0.002   0.000   HIS F  35 

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

*********************** 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  : 0.386 
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: 0.7173 (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: 0.7452 (tt0)
REVERT: F   98 ARG cc_start: 0.7910 (ptm160) cc_final: 0.7614 (ptt90)
  outliers start: 4
  outliers final: 1
  residues processed: 216
  average time/residue: 0.1075
  time to fit residues: 31.0293
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  : 0.319 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.4980
   chunk 97 optimal weight:    0.0070
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5998

-------------------------------------------------------------------------------
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
C 108 ASN
C 117 ASN
C 338 ASN
F 180 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.149339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.131388 restraints weight = 12146.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.11
r_work: 0.3502 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3347 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.3337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8786  Z= 0.170
  Angle     :  0.607  12.802  11914  Z= 0.314
  Chirality :  0.045   0.337   1349
  Planarity :  0.005   0.075   1504
  Dihedral  :  4.233  41.021   1195
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.69 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 25.75 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.26), residues: 1083
  helix:  1.57 (0.27), residues: 391
  sheet:  0.81 (0.32), residues: 264
  loop : -0.35 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  32 
 TYR   0.018   0.002   TYR F  59 
 PHE   0.021   0.002   PHE B 259 
 TRP   0.019   0.002   TRP C  80 
 HIS   0.004   0.001   HIS C 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 8785)
  covalent geometry    : angle       0.60706 (11912)
  SS BOND              : bond        0.00834 (    1)
  SS BOND              : angle       0.92168 (    2)
  hydrogen bonds       : bond        0.04558 (  416)
  hydrogen bonds       : angle       5.00623 ( 1182)

*********************** 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
  270 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 222
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   37 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6383 (mtm-85)
REVERT: A  119 LEU cc_start: 0.6977 (pt) cc_final: 0.6621 (pp)
REVERT: A  184 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6165 (tt)
REVERT: A  186 LEU cc_start: 0.7409 (tt) cc_final: 0.7188 (tp)
REVERT: A  267 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7218 (tt)
REVERT: A  270 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7209 (tt)
REVERT: A  273 TYR cc_start: 0.4911 (OUTLIER) cc_final: 0.4198 (p90)
REVERT: B   46 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.6457 (mttp)
REVERT: B  197 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7554 (mtpp)
REVERT: B  209 LYS cc_start: 0.7873 (ptmt) cc_final: 0.7552 (ptpp)
REVERT: B  259 PHE cc_start: 0.8158 (m-10) cc_final: 0.7741 (m-80)
REVERT: B  312 LYS cc_start: 0.7875 (mtmm) cc_final: 0.7647 (mttp)
REVERT: C   23 CYS cc_start: 0.7891 (m) cc_final: 0.7543 (m)
REVERT: C   66 ARG cc_start: 0.6458 (ttp-170) cc_final: 0.5847 (ttp80)
REVERT: C  327 THR cc_start: 0.8175 (m) cc_final: 0.7776 (p)
REVERT: F   39 GLN cc_start: 0.8088 (tt0) cc_final: 0.7875 (tt0)
  outliers start: 48
  outliers final: 22
  residues processed: 242
  average time/residue: 0.1005
  time to fit residues: 32.3523
Evaluate side-chains
  239 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 211
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ARG
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  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  247 MET
Chi-restraints excluded: chain B residue  269 ASN
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  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
Chi-restraints excluded: chain F residue  212 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0980
   chunk 66 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0060
   chunk 33 optimal weight:    0.0980
   chunk 42 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.0994

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
C 117 ASN
** C 338 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 = 0.3868 r_free = 0.3868 target = 0.145204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.127809 restraints weight = 12053.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.04
r_work: 0.3531 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
r_final: 0.3372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   8786  Z= 0.104
  Angle     :  0.520  10.598  11914  Z= 0.266
  Chirality :  0.041   0.271   1349
  Planarity :  0.005   0.066   1504
  Dihedral  :  3.804  31.474   1190
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.51 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 27.26 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.86 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1083
  helix:  1.77 (0.27), residues: 395
  sheet:  0.84 (0.32), residues: 264
  loop : -0.42 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  32 
 TYR   0.014   0.001   TYR F 221 
 PHE   0.010   0.001   PHE B 259 
 TRP   0.019   0.001   TRP A  75 
 HIS   0.003   0.001   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 8785)
  covalent geometry    : angle       0.51965 (11912)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       0.46597 (    2)
  hydrogen bonds       : bond        0.03677 (  416)
  hydrogen bonds       : angle       4.42725 ( 1182)

*********************** 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
  240 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 207
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.6852 (pt) cc_final: 0.6320 (pp)
REVERT: A  131 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6395 (mm)
REVERT: A  184 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6106 (tt)
REVERT: A  267 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7244 (tt)
REVERT: A  270 LEU cc_start: 0.7571 (tp) cc_final: 0.7321 (tt)
REVERT: A  273 TYR cc_start: 0.4959 (OUTLIER) cc_final: 0.4227 (p90)
REVERT: B  184 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.6079 (pt)
REVERT: B  197 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7421 (mtpp)
REVERT: B  209 LYS cc_start: 0.7738 (ptmt) cc_final: 0.7534 (ptmm)
REVERT: B  312 LYS cc_start: 0.7886 (mtmm) cc_final: 0.7479 (mttp)
REVERT: C   23 CYS cc_start: 0.7757 (m) cc_final: 0.7255 (m)
REVERT: C   47 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7333 (mpt180)
REVERT: C  327 THR cc_start: 0.8229 (m) cc_final: 0.7885 (p)
REVERT: F   95 TYR cc_start: 0.7989 (m-80) cc_final: 0.7771 (m-10)
REVERT: F  117 LEU cc_start: 0.6647 (tt) cc_final: 0.6443 (tp)
  outliers start: 33
  outliers final: 18
  residues processed: 219
  average time/residue: 0.0908
  time to fit residues: 26.8985
Evaluate side-chains
  224 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 200
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  267 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  184 ILE
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue   91 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  272 THR
Chi-restraints excluded: chain C residue  275 SER
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  115 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 36 optimal weight:    0.2980
   chunk 53 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0670
   chunk 57 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 11 optimal weight:    0.3980
   chunk 107 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
C  86 ASN
F 165 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.141855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.124497 restraints weight = 12254.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.06
r_work: 0.3492 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3337 r_free = 0.3337    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       32 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8786  Z= 0.132
  Angle     :  0.536   9.277  11914  Z= 0.273
  Chirality :  0.042   0.290   1349
  Planarity :  0.005   0.101   1504
  Dihedral  :  3.882  28.653   1190
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.42 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 25.43 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1083
  helix:  1.87 (0.27), residues: 396
  sheet:  0.70 (0.32), residues: 264
  loop : -0.40 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 248 
 TYR   0.012   0.001   TYR F 176 
 PHE   0.015   0.001   PHE C 197 
 TRP   0.018   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8785)
  covalent geometry    : angle       0.53633 (11912)
  SS BOND              : bond        0.00686 (    1)
  SS BOND              : angle       1.08632 (    2)
  hydrogen bonds       : bond        0.03522 (  416)
  hydrogen bonds       : angle       4.33084 ( 1182)

*********************** 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
  250 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 203
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  105 ILE cc_start: 0.8169 (mt) cc_final: 0.7798 (tt)
REVERT: A  136 MET cc_start: 0.7250 (tpp) cc_final: 0.6959 (tpp)
REVERT: A  184 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6148 (tt)
REVERT: A  216 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7390 (ttm170)
REVERT: A  270 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7509 (tt)
REVERT: A  273 TYR cc_start: 0.4929 (OUTLIER) cc_final: 0.4147 (p90)
REVERT: B   10 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8040 (mtpt)
REVERT: B   32 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7270 (ttm-80)
REVERT: B  197 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7416 (mtpp)
REVERT: B  209 LYS cc_start: 0.7741 (ptmt) cc_final: 0.7536 (ptmt)
REVERT: B  298 GLU cc_start: 0.6079 (pt0) cc_final: 0.5797 (pt0)
REVERT: B  312 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7662 (mttm)
REVERT: C   23 CYS cc_start: 0.7758 (m) cc_final: 0.7284 (m)
REVERT: C   35 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7554 (tp)
REVERT: C   47 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7185 (mpt180)
REVERT: C  168 ASP cc_start: 0.6660 (t0) cc_final: 0.6408 (t0)
REVERT: C  327 THR cc_start: 0.8242 (m) cc_final: 0.7796 (p)
REVERT: F   39 GLN cc_start: 0.8154 (tt0) cc_final: 0.7925 (tt0)
  outliers start: 47
  outliers final: 26
  residues processed: 229
  average time/residue: 0.0956
  time to fit residues: 29.5609
Evaluate side-chains
  234 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 201
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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  216 ARG
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   10 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  247 MET
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   91 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  155 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  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   93 MET
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0050
   chunk 89 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0770
   chunk 36 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.3552

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.141767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.124463 restraints weight = 12152.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.05
r_work: 0.3499 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3342
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3342 r_free = 0.3342    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       30 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3342 r_free = 0.3342    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.3342
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.2817

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= 0.115
  Angle     :  0.525  10.974  11914  Z= 0.266
  Chirality :  0.041   0.267   1349
  Planarity :  0.005   0.101   1504
  Dihedral  :  3.869  25.285   1190
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.23 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 25.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.26), residues: 1083
  helix:  1.93 (0.27), residues: 398
  sheet:  0.58 (0.31), residues: 266
  loop : -0.37 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 248 
 TYR   0.013   0.001   TYR F 176 
 PHE   0.015   0.001   PHE C 197 
 TRP   0.019   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8785)
  covalent geometry    : angle       0.52461 (11912)
  SS BOND              : bond        0.00543 (    1)
  SS BOND              : angle       0.85264 (    2)
  hydrogen bonds       : bond        0.03287 (  416)
  hydrogen bonds       : angle       4.19958 ( 1182)

*********************** 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
  254 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 205
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.7082 (mm) cc_final: 0.6861 (mp)
REVERT: A   77 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6911 (mm)
REVERT: A  105 ILE cc_start: 0.8137 (mt) cc_final: 0.7762 (tt)
REVERT: A  184 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6136 (tt)
REVERT: A  270 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7586 (tt)
REVERT: A  273 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.4206 (p90)
REVERT: B  197 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7399 (mtpp)
REVERT: B  209 LYS cc_start: 0.7748 (ptmt) cc_final: 0.7548 (ptmt)
REVERT: B  298 GLU cc_start: 0.6130 (pt0) cc_final: 0.5846 (pt0)
REVERT: B  312 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7659 (mttm)
REVERT: C   23 CYS cc_start: 0.7737 (m) cc_final: 0.7253 (m)
REVERT: C   35 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7553 (tp)
REVERT: C   47 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7264 (mpt180)
REVERT: C   68 LEU cc_start: 0.8419 (tt) cc_final: 0.8157 (tp)
REVERT: C   85 THR cc_start: 0.7830 (OUTLIER) cc_final: 0.7601 (t)
REVERT: C  168 ASP cc_start: 0.6683 (t0) cc_final: 0.6417 (t0)
REVERT: C  211 VAL cc_start: 0.7708 (t) cc_final: 0.7486 (m)
REVERT: C  264 HIS cc_start: 0.8886 (OUTLIER) cc_final: 0.8592 (t-90)
REVERT: C  327 THR cc_start: 0.8231 (m) cc_final: 0.7767 (p)
REVERT: F   39 GLN cc_start: 0.8162 (tt0) cc_final: 0.7952 (tt0)
REVERT: F  141 VAL cc_start: 0.7681 (p) cc_final: 0.7472 (m)
  outliers start: 49
  outliers final: 29
  residues processed: 234
  average time/residue: 0.0989
  time to fit residues: 31.2082
Evaluate side-chains
  241 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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   77 LEU
Chi-restraints excluded: chain A residue  183 CYS
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  232 VAL
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  187 THR
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  269 ASN
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   85 THR
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  155 ILE
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  282 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 89 optimal weight:    0.0070
   chunk 66 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 106 optimal weight:    0.4980
   chunk 92 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
B 269 ASN
F 165 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.140225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.122928 restraints weight = 12157.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 2.05
r_work: 0.3477 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3322
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3322
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8786  Z= 0.126
  Angle     :  0.544  11.812  11914  Z= 0.273
  Chirality :  0.042   0.260   1349
  Planarity :  0.005   0.102   1504
  Dihedral  :  3.924  24.095   1190
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.60 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 25.65 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.26), residues: 1083
  helix:  1.87 (0.27), residues: 404
  sheet:  0.53 (0.31), residues: 268
  loop : -0.32 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  32 
 TYR   0.010   0.001   TYR F 176 
 PHE   0.024   0.001   PHE B 334 
 TRP   0.019   0.001   TRP A  75 
 HIS   0.005   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8785)
  covalent geometry    : angle       0.54361 (11912)
  SS BOND              : bond        0.00675 (    1)
  SS BOND              : angle       1.09554 (    2)
  hydrogen bonds       : bond        0.03304 (  416)
  hydrogen bonds       : angle       4.20114 ( 1182)

*********************** 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
  261 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 212
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A   60 LEU cc_start: 0.7091 (mm) cc_final: 0.6835 (mp)
REVERT: A   77 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6988 (mm)
REVERT: A  105 ILE cc_start: 0.8146 (mt) cc_final: 0.7772 (tt)
REVERT: A  184 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6118 (tt)
REVERT: A  216 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7340 (ttm170)
REVERT: A  273 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.4260 (p90)
REVERT: B   46 LYS cc_start: 0.6656 (OUTLIER) cc_final: 0.6170 (mttm)
REVERT: B  197 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7394 (mtpp)
REVERT: B  209 LYS cc_start: 0.7766 (ptmt) cc_final: 0.7558 (ptmt)
REVERT: B  298 GLU cc_start: 0.6183 (pt0) cc_final: 0.5870 (pt0)
REVERT: B  312 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7631 (mttm)
REVERT: C   23 CYS cc_start: 0.7806 (m) cc_final: 0.7357 (m)
REVERT: C   35 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7591 (tp)
REVERT: C   47 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7281 (mpt180)
REVERT: C   59 MET cc_start: 0.8271 (tmm) cc_final: 0.8065 (tmm)
REVERT: C   68 LEU cc_start: 0.8421 (tt) cc_final: 0.8156 (tp)
REVERT: C   85 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7674 (t)
REVERT: C  168 ASP cc_start: 0.6681 (t0) cc_final: 0.6442 (t0)
REVERT: C  264 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8586 (t-90)
REVERT: C  316 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7891 (tp)
  outliers start: 49
  outliers final: 30
  residues processed: 240
  average time/residue: 0.1164
  time to fit residues: 37.1383
Evaluate side-chains
  248 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 208
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
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   77 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  216 ARG
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  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  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   85 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  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  231 CYS
Chi-restraints excluded: chain C residue  232 PHE
Chi-restraints excluded: chain C residue  264 HIS
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  316 LEU
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 68 optimal weight:    0.0030
   chunk 55 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0670
   chunk 90 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.3528

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

Flipped N/Q/H residues before XYZ refinement:
** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 165 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.140735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.123426 restraints weight = 12223.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.06
r_work: 0.3480 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8786  Z= 0.114
  Angle     :  0.540  12.492  11914  Z= 0.269
  Chirality :  0.041   0.249   1349
  Planarity :  0.005   0.098   1504
  Dihedral  :  3.902  24.262   1190
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.32 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 26.40 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.26), residues: 1083
  helix:  1.88 (0.27), residues: 404
  sheet:  0.57 (0.32), residues: 258
  loop : -0.36 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.011   0.001   TYR F 176 
 PHE   0.015   0.001   PHE C 197 
 TRP   0.020   0.001   TRP A  75 
 HIS   0.004   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8785)
  covalent geometry    : angle       0.53946 (11912)
  SS BOND              : bond        0.00574 (    1)
  SS BOND              : angle       0.94201 (    2)
  hydrogen bonds       : bond        0.03160 (  416)
  hydrogen bonds       : angle       4.14291 ( 1182)

*********************** 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
  250 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 205
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  105 ILE cc_start: 0.8122 (mt) cc_final: 0.7742 (tt)
REVERT: A  184 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6133 (tt)
REVERT: A  216 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7419 (ttm170)
REVERT: A  273 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.4266 (p90)
REVERT: B   46 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6131 (mttm)
REVERT: B  197 LYS cc_start: 0.7812 (mmtt) cc_final: 0.7422 (mtpp)
REVERT: B  209 LYS cc_start: 0.7817 (ptmt) cc_final: 0.7603 (ptmt)
REVERT: B  298 GLU cc_start: 0.6144 (pt0) cc_final: 0.5808 (pt0)
REVERT: B  312 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7620 (mttm)
REVERT: C   23 CYS cc_start: 0.7763 (m) cc_final: 0.7285 (m)
REVERT: C   35 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7556 (tp)
REVERT: C   47 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7203 (mpt180)
REVERT: C  168 ASP cc_start: 0.6785 (t0) cc_final: 0.6527 (t0)
REVERT: C  264 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (t-90)
REVERT: C  316 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7898 (tp)
  outliers start: 45
  outliers final: 29
  residues processed: 230
  average time/residue: 0.1045
  time to fit residues: 32.2846
Evaluate side-chains
  242 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 205
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
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  216 ARG
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  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  257 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  144 LEU
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  275 SER
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  316 LEU
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  115 THR
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 27 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0870
   chunk 13 optimal weight:    0.6980
   chunk 30 optimal weight:    0.2980
   chunk 97 optimal weight:    0.0000
   chunk 91 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.3362

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
C 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.141151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.123927 restraints weight = 12016.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.03
r_work: 0.3487 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3332 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3299 r_free = 0.3299    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3298 r_free = 0.3298    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3298
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8786  Z= 0.113
  Angle     :  0.554  12.663  11914  Z= 0.275
  Chirality :  0.041   0.240   1349
  Planarity :  0.005   0.096   1504
  Dihedral  :  3.906  24.081   1190
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.60 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.26), residues: 1083
  helix:  1.89 (0.27), residues: 404
  sheet:  0.49 (0.31), residues: 268
  loop : -0.35 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.010   0.001   TYR F 176 
 PHE   0.014   0.001   PHE C 197 
 TRP   0.021   0.001   TRP A  75 
 HIS   0.004   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8785)
  covalent geometry    : angle       0.55410 (11912)
  SS BOND              : bond        0.00591 (    1)
  SS BOND              : angle       0.95484 (    2)
  hydrogen bonds       : bond        0.03140 (  416)
  hydrogen bonds       : angle       4.12153 ( 1182)

*********************** 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
  253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 207
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  105 ILE cc_start: 0.8136 (mt) cc_final: 0.7767 (tt)
REVERT: A  184 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6122 (tt)
REVERT: A  216 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7395 (ttm170)
REVERT: A  273 TYR cc_start: 0.5173 (OUTLIER) cc_final: 0.4298 (p90)
REVERT: B   46 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6139 (mttm)
REVERT: B  197 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7413 (mtpp)
REVERT: B  209 LYS cc_start: 0.7765 (ptmt) cc_final: 0.7552 (ptmt)
REVERT: B  249 LEU cc_start: 0.7924 (tt) cc_final: 0.7721 (tp)
REVERT: B  298 GLU cc_start: 0.6290 (pt0) cc_final: 0.5942 (pt0)
REVERT: B  312 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7601 (mttm)
REVERT: C   23 CYS cc_start: 0.7820 (m) cc_final: 0.7354 (m)
REVERT: C   35 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7571 (tp)
REVERT: C   47 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7192 (mpt180)
REVERT: C  168 ASP cc_start: 0.6770 (t0) cc_final: 0.6518 (t0)
REVERT: C  316 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7858 (tp)
REVERT: C  327 THR cc_start: 0.8219 (m) cc_final: 0.7746 (p)
REVERT: F   67 ARG cc_start: 0.7661 (mtm110) cc_final: 0.7461 (mtm110)
  outliers start: 46
  outliers final: 35
  residues processed: 232
  average time/residue: 0.0989
  time to fit residues: 30.6122
Evaluate side-chains
  247 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 205
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
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  216 ARG
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  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  348 LEU
Chi-restraints excluded: chain C residue   16 ILE
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  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  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  316 LEU
Chi-restraints excluded: chain C residue  320 ASP
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  115 THR
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 80 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 97 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0570
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 89 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
F  39 GLN
F 165 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.139225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.122004 restraints weight = 12082.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.05
r_work: 0.3461 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    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 = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.3397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8786  Z= 0.135
  Angle     :  0.572  12.949  11914  Z= 0.284
  Chirality :  0.042   0.235   1349
  Planarity :  0.005   0.091   1504
  Dihedral  :  4.024  24.156   1190
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.69 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 26.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.26), residues: 1083
  helix:  1.87 (0.27), residues: 404
  sheet:  0.51 (0.32), residues: 254
  loop : -0.37 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 248 
 TYR   0.012   0.001   TYR F 101 
 PHE   0.015   0.001   PHE C 197 
 TRP   0.015   0.001   TRP C  80 
 HIS   0.004   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8785)
  covalent geometry    : angle       0.57159 (11912)
  SS BOND              : bond        0.00701 (    1)
  SS BOND              : angle       1.13814 (    2)
  hydrogen bonds       : bond        0.03261 (  416)
  hydrogen bonds       : angle       4.19559 ( 1182)

*********************** 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
  247 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 204
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  105 ILE cc_start: 0.8111 (mt) cc_final: 0.7729 (tt)
REVERT: A  184 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6107 (tt)
REVERT: A  216 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7395 (ttm170)
REVERT: A  273 TYR cc_start: 0.5306 (OUTLIER) cc_final: 0.4350 (p90)
REVERT: B   46 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6269 (mttm)
REVERT: B  197 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7413 (mtpp)
REVERT: B  209 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7630 (ptmt)
REVERT: B  298 GLU cc_start: 0.6371 (pt0) cc_final: 0.6019 (pt0)
REVERT: B  312 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7624 (mttm)
REVERT: C   23 CYS cc_start: 0.7845 (m) cc_final: 0.7390 (m)
REVERT: C   35 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7548 (tp)
REVERT: C   47 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7167 (mpt180)
REVERT: C  168 ASP cc_start: 0.6851 (t0) cc_final: 0.6628 (t0)
REVERT: C  316 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7907 (tp)
  outliers start: 43
  outliers final: 33
  residues processed: 227
  average time/residue: 0.0979
  time to fit residues: 29.9871
Evaluate side-chains
  244 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 204
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
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  216 ARG
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  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  269 ASN
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  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  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  316 LEU
Chi-restraints excluded: chain C residue  320 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    0.0870
   chunk 98 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.138154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.120868 restraints weight = 12013.792|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.04
r_work: 0.3446 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3268
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3268 r_free = 0.3268    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 = 0.3268 r_free = 0.3268    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3268
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8786  Z= 0.169
  Angle     :  0.602  13.033  11914  Z= 0.300
  Chirality :  0.044   0.251   1349
  Planarity :  0.005   0.092   1504
  Dihedral  :  4.190  24.383   1190
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.97 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 27.26 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.26), residues: 1083
  helix:  1.77 (0.27), residues: 404
  sheet:  0.35 (0.32), residues: 260
  loop : -0.36 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 248 
 TYR   0.015   0.001   TYR F 213 
 PHE   0.018   0.002   PHE C 197 
 TRP   0.014   0.002   TRP C  80 
 HIS   0.004   0.001   HIS B 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 8785)
  covalent geometry    : angle       0.60137 (11912)
  SS BOND              : bond        0.00831 (    1)
  SS BOND              : angle       1.35290 (    2)
  hydrogen bonds       : bond        0.03449 (  416)
  hydrogen bonds       : angle       4.30772 ( 1182)

********************** 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
  259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 219
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ILE cc_start: 0.8100 (mt) cc_final: 0.7709 (tt)
REVERT: A  184 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6128 (tt)
REVERT: A  273 TYR cc_start: 0.5350 (OUTLIER) cc_final: 0.4432 (p90)
REVERT: B   46 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6370 (mttm)
REVERT: B  197 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7423 (mtpp)
REVERT: B  209 LYS cc_start: 0.7916 (ptmt) cc_final: 0.7686 (ptmt)
REVERT: B  249 LEU cc_start: 0.7894 (tt) cc_final: 0.7664 (tp)
REVERT: B  253 ILE cc_start: 0.7780 (pt) cc_final: 0.7386 (mm)
REVERT: B  298 GLU cc_start: 0.6388 (pt0) cc_final: 0.6048 (pt0)
REVERT: B  308 GLU cc_start: 0.7572 (tt0) cc_final: 0.7319 (tt0)
REVERT: B  312 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7613 (mttm)
REVERT: C   23 CYS cc_start: 0.7810 (m) cc_final: 0.7324 (m)
REVERT: C   35 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7566 (tp)
REVERT: C   47 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7099 (mpt180)
REVERT: C  168 ASP cc_start: 0.6897 (t0) cc_final: 0.6652 (t0)
REVERT: C  316 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7930 (tp)
REVERT: F  213 TYR cc_start: 0.7899 (m-80) cc_final: 0.7619 (m-80)
REVERT: F  223 LEU cc_start: 0.7954 (mp) cc_final: 0.7638 (mt)
  outliers start: 40
  outliers final: 33
  residues processed: 243
  average time/residue: 0.1015
  time to fit residues: 33.0709
Evaluate side-chains
  253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 214
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 TYR
Chi-restraints excluded: chain A residue   91 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  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  187 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  331 ASN
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  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  275 SER
Chi-restraints excluded: chain C residue  282 LEU
Chi-restraints excluded: chain C residue  292 CYS
Chi-restraints excluded: chain C residue  316 LEU
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  201 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.136791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.119581 restraints weight = 12070.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 2.04
r_work: 0.3426 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3270
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3270 r_free = 0.3270    target_work(ls_wunit_k1) = 0.103         |
| 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) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       31 |
|-----------------------------------------------------------------------------|
r_final: 0.3269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8786  Z= 0.187
  Angle     :  0.610  13.011  11914  Z= 0.306
  Chirality :  0.044   0.197   1349
  Planarity :  0.005   0.080   1504
  Dihedral  :  4.370  24.834   1190
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 27.91 %
    Favored  : 67.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.26), residues: 1083
  helix:  1.67 (0.27), residues: 402
  sheet:  0.27 (0.32), residues: 259
  loop : -0.47 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 217 
 TYR   0.021   0.002   TYR F 176 
 PHE   0.020   0.002   PHE C 197 
 TRP   0.014   0.002   TRP C  80 
 HIS   0.006   0.001   HIS C 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 8785)
  covalent geometry    : angle       0.60959 (11912)
  SS BOND              : bond        0.00886 (    1)
  SS BOND              : angle       1.36304 (    2)
  hydrogen bonds       : bond        0.03589 (  416)
  hydrogen bonds       : angle       4.40927 ( 1182)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2493.92 seconds
wall clock time: 43 minutes 22.92 seconds (2602.92 seconds total)