Starting phenix.real_space_refine
on Wed Mar  4 20:47:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xis_22199/03_2026/6xis_22199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xis_22199/03_2026/6xis_22199.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xis_22199/03_2026/6xis_22199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xis_22199/03_2026/6xis_22199.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xis_22199/03_2026/6xis_22199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xis_22199/03_2026/6xis_22199.map"
  }
  resolution = 3.9
  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=   0.002 sd=   0.061
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8723 atoms to isotropic.
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      52      5.16       5
     C    6086      2.51       5
     N    1548      2.21       5
     O    1750      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9436
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2357
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 9, 'TRANS': 300}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 144
          Unresolved non-hydrogen angles: 179
          Unresolved non-hydrogen dihedrals: 123
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 79
    Chain: "B"
      Number of atoms: 2361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2361
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 9, 'TRANS': 300}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 141
          Unresolved non-hydrogen angles: 178
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 80
    Chain: "C"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2357
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 9, 'TRANS': 300}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 146
          Unresolved non-hydrogen angles: 184
          Unresolved non-hydrogen dihedrals: 128
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 2, 'PHE:plan': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 84
    Chain: "D"
      Number of atoms: 2361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2361
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 9, 'TRANS': 300}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 180
          Unresolved non-hydrogen dihedrals: 123
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'PHE:plan': 3, 'HIS:plan': 1, 'GLU:plan': 5, 'TRP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 81
  Time building chain proxies: 2.41, per 1000 atoms: 0.26
  Number of scatterers: 9436
  At special positions: 0
  Unit cell: (90.3, 90.3, 138.03, 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      52     16.00
     O    1750      8.00
     N    1548      7.00
     C    6086      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS A 166 " distance=1.57
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 166 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 134 " - pdb=" SG  CYS C 166 " distance=2.07
    Simple disulfide: pdb=" SG  CYS D 134 " - pdb=" SG  CYS D 166 " 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: 0.76
  Conformation dependent library (CDL) restraints added in 495.0 milliseconds
  

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2336

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 23 sheets defined
      32.1% alpha, 27.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 78 through 88
      removed outlier: 3.799A  pdb=" N   ASP A  88 " --> pdb=" O   THR A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 117
    Processing helix  chain 'A' and resid 119 through 128
      removed outlier: 4.552A  pdb=" N   MET A 123 " --> pdb=" O   ILE A 119 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ASP A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   HIS A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLU A 127 " --> pdb=" O   MET A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 153
      removed outlier: 3.891A  pdb=" N   SER A 148 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 196
      removed outlier: 4.090A  pdb=" N   LEU A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 381
    Processing helix  chain 'B' and resid 80 through 87
      removed outlier: 3.584A  pdb=" N   VAL B  87 " --> pdb=" O   PHE B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 117
      removed outlier: 3.652A  pdb=" N   TYR B 102 " --> pdb=" O   PHE B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 153
    Processing helix  chain 'B' and resid 170 through 196
    Processing helix  chain 'B' and resid 368 through 381
    Processing helix  chain 'C' and resid 78 through 88
      removed outlier: 3.508A  pdb=" N   ILE C  82 " --> pdb=" O   TYR C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 117
      removed outlier: 3.549A  pdb=" N   TYR C 102 " --> pdb=" O   PHE C  98 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE C 116 " --> pdb=" O   ILE C 112 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA C 117 " --> pdb=" O   TRP C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 122
      removed outlier: 4.383A  pdb=" N   ASP C 122 " --> pdb=" O   TYR C 118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 3.643A  pdb=" N   TRP C 131 " --> pdb=" O   ASP C 128 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 153
      removed outlier: 3.784A  pdb=" N   SER C 148 " --> pdb=" O   ALA C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 196
      removed outlier: 3.890A  pdb=" N   LEU C 174 " --> pdb=" O   ILE C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 302
      removed outlier: 3.953A  pdb=" N   LYS C 301 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 328 through 332
    Processing helix  chain 'C' and resid 353 through 358
      removed outlier: 4.214A  pdb=" N   HIS C 357 " --> pdb=" O   TYR C 353 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLU C 358 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 353 through 358'
    Processing helix  chain 'C' and resid 368 through 381
    Processing helix  chain 'D' and resid 80 through 88
      removed outlier: 3.512A  pdb=" N   THR D  84 " --> pdb=" O   THR D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 117
    Processing helix  chain 'D' and resid 144 through 153
    Processing helix  chain 'D' and resid 170 through 196
      removed outlier: 3.871A  pdb=" N   LEU D 174 " --> pdb=" O   ILE D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 328 through 332
      removed outlier: 3.522A  pdb=" N   ILE D 332 " --> pdb=" O   THR D 329 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 368 through 381
    Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 207
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 262
      removed outlier: 4.571A  pdb=" N   ALA A 241 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   VAL A 235 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU A 275 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 262
      removed outlier: 4.571A  pdb=" N   ALA A 241 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   ALA A 237 " --> pdb=" O   GLU A 311 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   GLU A 311 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   ILE A 239 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE A 309 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ALA A 241 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL A 307 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   LEU A 243 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   GLU A 305 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338
    Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345
    Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 207
    Processing sheet with id=AA8, first strand: chain 'B' and resid 205 through 207
    Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 262
      removed outlier: 5.326A  pdb=" N   LYS B 247 " --> pdb=" O   PRO B 256 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   ALA B 241 " --> pdb=" O   ILE B 262 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY B 312 " --> pdb=" O   CYS B 321 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 336 through 338
    Processing sheet with id=AB2, first strand: chain 'B' and resid 342 through 345
    Processing sheet with id=AB3, first strand: chain 'C' and resid 205 through 207
    Processing sheet with id=AB4, first strand: chain 'C' and resid 205 through 207
    Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 262
      removed outlier: 5.346A  pdb=" N   LYS C 247 " --> pdb=" O   PRO C 256 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ALA C 241 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   VAL C 235 " --> pdb=" O   LEU C 275 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   LEU C 275 " --> pdb=" O   VAL C 235 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 254 through 262
      removed outlier: 5.346A  pdb=" N   LYS C 247 " --> pdb=" O   PRO C 256 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ALA C 241 " --> pdb=" O   ILE C 262 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   GLU C 236 " --> pdb=" O   MET C 313 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   MET C 313 " --> pdb=" O   GLU C 236 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 338
    Processing sheet with id=AB8, first strand: chain 'C' and resid 342 through 345
    Processing sheet with id=AB9, first strand: chain 'D' and resid 205 through 207
    Processing sheet with id=AC1, first strand: chain 'D' and resid 205 through 207
    Processing sheet with id=AC2, first strand: chain 'D' and resid 258 through 262
      removed outlier: 4.554A  pdb=" N   ALA D 241 " --> pdb=" O   ILE D 262 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU D 273 " --> pdb=" O   ALA D 237 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 258 through 262
      removed outlier: 4.554A  pdb=" N   ALA D 241 " --> pdb=" O   ILE D 262 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ALA D 237 " --> pdb=" O   GLU D 311 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   GLU D 311 " --> pdb=" O   ALA D 237 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ILE D 239 " --> pdb=" O   ILE D 309 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   ILE D 309 " --> pdb=" O   ILE D 239 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ALA D 241 " --> pdb=" O   VAL D 307 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   VAL D 307 " --> pdb=" O   ALA D 241 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   LEU D 243 " --> pdb=" O   GLU D 305 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   GLU D 305 " --> pdb=" O   LEU D 243 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 336 through 338
    Processing sheet with id=AC5, first strand: chain 'D' and resid 342 through 345

    441 hydrogen bonds defined for protein.
    1236 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: 1.59

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1533
        1.31 -     1.43: 2613
        1.43 -     1.56: 5405
        1.56 -     1.69: 0
        1.69 -     1.82: 80
  Bond restraints: 9631
  Sorted by residual:
  bond pdb=" C   GLY D 110 "
       pdb=" N   MET D 111 "
    ideal  model  delta    sigma   weight residual
    1.334  1.239  0.095 1.27e-02 6.20e+03 5.61e+01
  bond pdb=" C   MET D 111 "
       pdb=" N   ILE D 112 "
    ideal  model  delta    sigma   weight residual
    1.335  1.426 -0.091 1.26e-02 6.30e+03 5.18e+01
  bond pdb=" C   PRO D 365 "
       pdb=" O   PRO D 365 "
    ideal  model  delta    sigma   weight residual
    1.233  1.177  0.056 1.12e-02 7.97e+03 2.51e+01
  bond pdb=" N   ILE C 255 "
       pdb=" CA  ILE C 255 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.031 7.60e-03 1.73e+04 1.71e+01
  bond pdb=" N   ASP D 122 "
       pdb=" CA  ASP D 122 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.035 9.00e-03 1.23e+04 1.55e+01
  ... (remaining 9626 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 11161
        1.94 -     3.88: 1764
        3.88 -     5.83: 174
        5.83 -     7.77: 17
        7.77 -     9.71: 3
  Bond angle restraints: 13119
  Sorted by residual:
  angle pdb=" N   PRO C 133 "
        pdb=" CA  PRO C 133 "
        pdb=" CB  PRO C 133 "
      ideal   model   delta    sigma   weight residual
     103.25  111.55   -8.30 1.05e+00 9.07e-01 6.25e+01
  angle pdb=" N   PRO D 133 "
        pdb=" CA  PRO D 133 "
        pdb=" CB  PRO D 133 "
      ideal   model   delta    sigma   weight residual
     103.25  111.17   -7.92 1.05e+00 9.07e-01 5.69e+01
  angle pdb=" N   PRO B 133 "
        pdb=" CA  PRO B 133 "
        pdb=" CB  PRO B 133 "
      ideal   model   delta    sigma   weight residual
     103.25  110.84   -7.59 1.05e+00 9.07e-01 5.22e+01
  angle pdb=" N   PRO A 133 "
        pdb=" CA  PRO A 133 "
        pdb=" CB  PRO A 133 "
      ideal   model   delta    sigma   weight residual
     103.25  110.60   -7.35 1.05e+00 9.07e-01 4.90e+01
  angle pdb=" N   TYR D 159 "
        pdb=" CA  TYR D 159 "
        pdb=" C   TYR D 159 "
      ideal   model   delta    sigma   weight residual
     111.28  103.74    7.54 1.09e+00 8.42e-01 4.79e+01
  ... (remaining 13114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.18: 5041
       16.18 -    32.36: 459
       32.36 -    48.54: 109
       48.54 -    64.72: 20
       64.72 -    80.90: 12
  Dihedral angle restraints: 5641
    sinusoidal: 2029
      harmonic: 3612
  Sorted by residual:
  dihedral pdb=" CB  CYS D 134 "
           pdb=" SG  CYS D 134 "
           pdb=" SG  CYS D 166 "
           pdb=" CB  CYS D 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.68  -77.68     1      1.00e+01 1.00e-02 7.55e+01
  dihedral pdb=" CB  CYS A 134 "
           pdb=" SG  CYS A 134 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.27   68.27     1      1.00e+01 1.00e-02 6.05e+01
  dihedral pdb=" CB  CYS C 134 "
           pdb=" SG  CYS C 134 "
           pdb=" SG  CYS C 166 "
           pdb=" CB  CYS C 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.47   64.53     1      1.00e+01 1.00e-02 5.47e+01
  ... (remaining 5638 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 894
       0.053 -    0.106: 344
       0.106 -    0.160: 210
       0.160 -    0.213: 83
       0.213 -    0.266: 26
  Chirality restraints: 1557
  Sorted by residual:
  chirality pdb=" CA  ILE C 255 "
            pdb=" N   ILE C 255 "
            pdb=" C   ILE C 255 "
            pdb=" CB  ILE C 255 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  VAL D 276 "
            pdb=" N   VAL D 276 "
            pdb=" C   VAL D 276 "
            pdb=" CB  VAL D 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  CYS A 134 "
            pdb=" N   CYS A 134 "
            pdb=" C   CYS A 134 "
            pdb=" CB  CYS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 1554 not shown)

  Planarity restraints: 1640
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 263 "    0.019 2.00e-02 2.50e+03   3.78e-02 1.43e+01
        pdb=" C   ASN C 263 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   ASN C 263 "    0.024 2.00e-02 2.50e+03
        pdb=" N   VAL C 264 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D 263 "    0.017 2.00e-02 2.50e+03   3.41e-02 1.16e+01
        pdb=" C   ASN D 263 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   ASN D 263 "    0.022 2.00e-02 2.50e+03
        pdb=" N   VAL D 264 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D 165 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   LYS D 165 "    0.057 2.00e-02 2.50e+03
        pdb=" O   LYS D 165 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   CYS D 166 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1637 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1198
        2.76 -     3.30: 9919
        3.30 -     3.83: 15257
        3.83 -     4.37: 18172
        4.37 -     4.90: 29637
  Nonbonded interactions: 74183
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 377 "
            pdb=" N   ARG B 378 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" N   GLN A 288 "
            pdb=" OE1 GLN A 288 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" SG  CYS A 221 "
            pdb=" OG  SER A 282 "
     model   vdw
     2.259 3.400
  nonbonded pdb=" O   LEU A 299 "
            pdb=" OG1 THR A 329 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" NH2 ARG A 337 "
            pdb=" OE1 GLU B 251 "
     model   vdw
     2.281 3.120
  ... (remaining 74178 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 55 through 57 or (resid 58 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 59 through 77 or (resid 78 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 79 through 80 or (resid 81 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 82 through 104 or ( \ 
resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106  \ 
through 111 or (resid 112 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 113 through 124 or (resid 125 through 128 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 129 through 150 or (resid 151 through 15 \ 
2 and (name N or name CA or name C or name O or name CB )) or resid 153 through  \ 
162 or (resid 163 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 164 through 274 or (resid 275 and (name N or name CA or name C or name O or  \ 
name CB )) or resid 276 through 314 or (resid 315 through 316 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 317 through 348 or (resid 349 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 350 through 381) \ 
)
  selection = (chain 'B' and (resid 55 through 77 or (resid 78 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 79 through 104 or (resid 105 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 106 through 124 or (resid 125  \ 
through 128 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 
9 through 150 or (resid 151 through 152 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 153 through 162 or (resid 163 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 164 through 171 or (resid 172 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 173 through 175 or (re \ 
sid 176 and (name N or name CA or name C or name O or name CB )) or resid 177 th \ 
rough 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 226 through 274 or (resid 275 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 276 through 348 or (resid 349 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 350 through 369 or (resid 370 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 371 through 381))
  selection = (chain 'C' and (resid 55 through 57 or (resid 58 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 59 through 80 or (resid 81 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 82 through 111 or (resid 112 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 113 through 124 o \ 
r (resid 125 through 128 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 129 through 150 or (resid 151 through 152 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 153 through 154 or (resid 155 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 156 through 162 or (resid \ 
 163 and (name N or name CA or name C or name O or name CB )) or resid 164 throu \ 
gh 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 173 through 175 or (resid 176 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 177 through 224 or (resid 225 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 226 through 274 or (resid 275 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 276 through 381))
  selection = (chain 'D' and (resid 55 through 57 or (resid 58 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 59 through 77 or (resid 78 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 79 through 86 or (resid 87 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 88 through 104 or ( \ 
resid 105 and (name N or name CA or name C or name O or name CB )) or resid 106  \ 
through 111 or (resid 112 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 113 through 151 or (resid 152 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 153 through 154 or (resid 155 and (name N or name CA \ 
 or name C or name O or name CB )) or resid 156 through 171 or (resid 172 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 173 through 175 or ( \ 
resid 176 and (name N or name CA or name C or name O or name CB )) or resid 177  \ 
through 224 or (resid 225 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 226 through 314 or (resid 315 through 316 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 317 through 369 or (resid 370 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 371 through 381))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.560
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
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      :  0.010   0.461   9635  Z= 0.715
  Angle     :  1.355  25.880  13127  Z= 1.048
  Chirality :  0.082   0.266   1557
  Planarity :  0.007   0.038   1640
  Dihedral  : 13.731  80.902   3293
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  1.81 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 10.50 %
    Favored  : 86.30 %
  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 are not related in a simple way.
  whole:  0.47 (0.23), residues: 1216
  helix:  2.62 (0.25), residues: 340
  sheet:  0.88 (0.33), residues: 237
  loop : -1.29 (0.22), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  60 
 TYR   0.017   0.002   TYR C 157 
 PHE   0.021   0.002   PHE D 147 
 TRP   0.029   0.002   TRP B 114 
 HIS   0.004   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00888 ( 9631)
  covalent geometry    : angle       1.32929 (13119)
  SS BOND              : bond        0.23120 (    4)
  SS BOND              : angle      10.72136 (    8)
  hydrogen bonds       : bond        0.16841 (  418)
  hydrogen bonds       : angle       7.31289 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 327
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 LYS cc_start: 0.7964 (mmtp) cc_final: 0.7660 (mtpp)
REVERT: A  322 GLN cc_start: 0.7028 (tt0) cc_final: 0.6821 (mp10)
REVERT: A  356 PHE cc_start: 0.8614 (t80) cc_final: 0.8318 (t80)
REVERT: A  363 SER cc_start: 0.5593 (t) cc_final: 0.5090 (t)
REVERT: B  289 SER cc_start: 0.8466 (p) cc_final: 0.8183 (p)
REVERT: C  149 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7764 (mt)
REVERT: C  255 ILE cc_start: 0.8577 (mt) cc_final: 0.8353 (mt)
REVERT: C  257 LEU cc_start: 0.7329 (tp) cc_final: 0.6876 (tt)
REVERT: C  259 GLN cc_start: 0.7476 (mt0) cc_final: 0.7125 (mt0)
REVERT: C  261 ASP cc_start: 0.8279 (t0) cc_final: 0.7620 (t0)
REVERT: D  161 VAL cc_start: 0.7359 (OUTLIER) cc_final: 0.7034 (t)
REVERT: D  164 ASP cc_start: 0.5349 (m-30) cc_final: 0.4152 (m-30)
REVERT: D  270 ASP cc_start: 0.7148 (m-30) cc_final: 0.6812 (t0)
REVERT: D  327 TYR cc_start: 0.7629 (m-80) cc_final: 0.7305 (m-80)
  outliers start: 31
  outliers final: 7
  residues processed: 346
  average time/residue: 0.0902
  time to fit residues: 44.5692
Evaluate side-chains
  211 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 202
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain C residue  134 CYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  166 CYS
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain D residue  161 VAL
Chi-restraints excluded: chain D residue  192 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0010
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
C  66 ASN
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 ASN
D 139 ASN
D 176 GLN
** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 287 GLN
D 357 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.152069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132119 restraints weight = 19012.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.134466 restraints weight = 13178.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.136113 restraints weight = 10279.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.137258 restraints weight = 8625.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.137924 restraints weight = 7650.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9635  Z= 0.156
  Angle     :  0.698  10.491  13127  Z= 0.363
  Chirality :  0.046   0.166   1557
  Planarity :  0.004   0.040   1640
  Dihedral  :  5.714  56.754   1337
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  2.71 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.82 %
    Favored  : 78.78 %
  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 are not related in a simple way.
  whole:  0.42 (0.24), residues: 1216
  helix:  2.32 (0.27), residues: 344
  sheet:  0.83 (0.34), residues: 237
  loop : -1.17 (0.23), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 272 
 TYR   0.036   0.002   TYR D 157 
 PHE   0.018   0.002   PHE A 145 
 TRP   0.042   0.002   TRP B 106 
 HIS   0.004   0.001   HIS D 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9631)
  covalent geometry    : angle       0.69353 (13119)
  SS BOND              : bond        0.00870 (    4)
  SS BOND              : angle       3.33440 (    8)
  hydrogen bonds       : bond        0.04981 (  418)
  hydrogen bonds       : angle       5.50966 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 222
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.7021 (mtt) cc_final: 0.6817 (ptp)
REVERT: A  322 GLN cc_start: 0.7827 (tt0) cc_final: 0.7297 (mp10)
REVERT: A  356 PHE cc_start: 0.8887 (t80) cc_final: 0.8459 (t80)
REVERT: B  106 TRP cc_start: 0.8609 (m-90) cc_final: 0.8279 (m-90)
REVERT: B  187 MET cc_start: 0.8166 (tpp) cc_final: 0.7722 (tpt)
REVERT: B  215 MET cc_start: 0.8492 (tpp) cc_final: 0.8167 (tpp)
REVERT: B  289 SER cc_start: 0.8663 (p) cc_final: 0.8282 (p)
REVERT: B  370 LYS cc_start: 0.7267 (tmmt) cc_final: 0.7052 (tmtt)
REVERT: C  149 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8602 (mt)
REVERT: C  288 GLN cc_start: 0.9072 (mp10) cc_final: 0.8691 (mp10)
REVERT: C  344 LEU cc_start: 0.5890 (OUTLIER) cc_final: 0.5600 (mp)
REVERT: D  100 MET cc_start: 0.7272 (mtt) cc_final: 0.7049 (ptp)
REVERT: D  226 VAL cc_start: 0.9149 (t) cc_final: 0.8910 (p)
  outliers start: 33
  outliers final: 23
  residues processed: 244
  average time/residue: 0.0814
  time to fit residues: 29.4612
Evaluate side-chains
  207 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 182
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain C residue  134 CYS
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  164 ASP
Chi-restraints excluded: chain C residue  166 CYS
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  213 ILE
Chi-restraints excluded: chain C residue  258 ASN
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  139 ASN
Chi-restraints excluded: chain D residue  192 PHE
Chi-restraints excluded: chain D residue  247 LYS
Chi-restraints excluded: chain D residue  304 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 114 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0050
   chunk 120 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    2.8002

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.138805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.117987 restraints weight = 19098.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.120199 restraints weight = 13342.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.121664 restraints weight = 10532.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.122686 restraints weight = 9002.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.123368 restraints weight = 8079.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   9635  Z= 0.303
  Angle     :  0.810  10.804  13127  Z= 0.437
  Chirality :  0.049   0.173   1557
  Planarity :  0.005   0.045   1640
  Dihedral  :  6.454  50.051   1333
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.28 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 19.88 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -0.35 (0.23), residues: 1216
  helix:  1.56 (0.26), residues: 353
  sheet:  0.34 (0.34), residues: 231
  loop : -1.57 (0.23), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 378 
 TYR   0.021   0.002   TYR B 360 
 PHE   0.023   0.003   PHE A 254 
 TRP   0.034   0.003   TRP D 334 
 HIS   0.009   0.003   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00646 ( 9631)
  covalent geometry    : angle       0.80196 (13119)
  SS BOND              : bond        0.02503 (    4)
  SS BOND              : angle       4.58409 (    8)
  hydrogen bonds       : bond        0.05044 (  418)
  hydrogen bonds       : angle       5.65615 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 198
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  106 TRP cc_start: 0.8616 (m-10) cc_final: 0.8414 (m-10)
REVERT: A  215 MET cc_start: 0.7442 (mmm) cc_final: 0.6957 (tpp)
REVERT: A  322 GLN cc_start: 0.8041 (tt0) cc_final: 0.7713 (mp10)
REVERT: B  106 TRP cc_start: 0.8669 (m-10) cc_final: 0.8251 (m-90)
REVERT: B  187 MET cc_start: 0.8194 (tpp) cc_final: 0.7836 (tpp)
REVERT: B  215 MET cc_start: 0.8590 (tpp) cc_final: 0.8285 (tpp)
REVERT: C  149 ILE cc_start: 0.8938 (mm) cc_final: 0.8709 (mt)
REVERT: C  157 TYR cc_start: 0.7721 (m-80) cc_final: 0.7511 (m-80)
REVERT: C  176 GLN cc_start: 0.8167 (tt0) cc_final: 0.7617 (mt0)
REVERT: C  187 MET cc_start: 0.8036 (tpt) cc_final: 0.7421 (tmm)
REVERT: C  257 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7638 (tt)
REVERT: D  150 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7938 (mt-10)
REVERT: D  213 ILE cc_start: 0.8321 (tp) cc_final: 0.8043 (tt)
  outliers start: 51
  outliers final: 36
  residues processed: 227
  average time/residue: 0.0859
  time to fit residues: 28.3726
Evaluate side-chains
  207 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASP
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  208 SER
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  192 PHE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain C residue  125 HIS
Chi-restraints excluded: chain C residue  164 ASP
Chi-restraints excluded: chain C residue  166 CYS
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain D residue  139 ASN
Chi-restraints excluded: chain D residue  247 LYS
Chi-restraints excluded: chain D residue  270 ASP
Chi-restraints excluded: chain D residue  274 PHE
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  351 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 116 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
C  94 ASN
** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 ASN
** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.143172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.121831 restraints weight = 19180.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.124389 restraints weight = 13004.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.126029 restraints weight = 9989.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.126736 restraints weight = 8394.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.127843 restraints weight = 7627.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.4350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   9635  Z= 0.158
  Angle     :  0.668   9.341  13127  Z= 0.353
  Chirality :  0.045   0.186   1557
  Planarity :  0.004   0.077   1640
  Dihedral  :  5.384  44.723   1324
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.70 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 21.42 %
    Favored  : 73.94 %
  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 are not related in a simple way.
  whole: -0.21 (0.24), residues: 1216
  helix:  1.84 (0.27), residues: 349
  sheet:  0.15 (0.34), residues: 233
  loop : -1.47 (0.24), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 324 
 TYR   0.021   0.001   TYR A 157 
 PHE   0.018   0.002   PHE A 254 
 TRP   0.015   0.002   TRP C 106 
 HIS   0.004   0.001   HIS D 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 9631)
  covalent geometry    : angle       0.66159 (13119)
  SS BOND              : bond        0.00541 (    4)
  SS BOND              : angle       3.71492 (    8)
  hydrogen bonds       : bond        0.04238 (  418)
  hydrogen bonds       : angle       5.10499 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 189
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LEU cc_start: 0.7632 (mm) cc_final: 0.7341 (mm)
REVERT: A  215 MET cc_start: 0.6747 (mmm) cc_final: 0.6466 (tpp)
REVERT: B  106 TRP cc_start: 0.8540 (m-10) cc_final: 0.8134 (m-90)
REVERT: B  187 MET cc_start: 0.8113 (tpp) cc_final: 0.7733 (tpp)
REVERT: B  215 MET cc_start: 0.8524 (tpp) cc_final: 0.8155 (tpp)
REVERT: B  311 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6615 (tt0)
REVERT: B  370 LYS cc_start: 0.7466 (tmmt) cc_final: 0.7264 (tmmt)
REVERT: C  149 ILE cc_start: 0.8930 (mm) cc_final: 0.8612 (mt)
REVERT: C  176 GLN cc_start: 0.8225 (tt0) cc_final: 0.7791 (mt0)
REVERT: C  240 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7538 (mtm110)
REVERT: D  150 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8000 (mt-10)
  outliers start: 45
  outliers final: 29
  residues processed: 214
  average time/residue: 0.0752
  time to fit residues: 24.3572
Evaluate side-chains
  204 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain C residue  125 HIS
Chi-restraints excluded: chain C residue  166 CYS
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  223 MET
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain C residue  339 THR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  247 LYS
Chi-restraints excluded: chain D residue  274 PHE
Chi-restraints excluded: chain D residue  304 LEU
Chi-restraints excluded: chain D residue  351 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 70 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0870
   chunk 33 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.6962

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.144498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.123802 restraints weight = 18947.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.126033 restraints weight = 13404.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.127523 restraints weight = 10587.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.128564 restraints weight = 9048.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.129097 restraints weight = 8100.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.4707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9635  Z= 0.134
  Angle     :  0.633   8.770  13127  Z= 0.331
  Chirality :  0.044   0.179   1557
  Planarity :  0.004   0.044   1640
  Dihedral  :  5.012  38.961   1324
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.61 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 22.45 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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 are not related in a simple way.
  whole: -0.18 (0.24), residues: 1216
  helix:  1.97 (0.28), residues: 343
  sheet:  0.13 (0.34), residues: 231
  loop : -1.45 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 324 
 TYR   0.027   0.001   TYR A 157 
 PHE   0.015   0.001   PHE A 254 
 TRP   0.023   0.001   TRP C 106 
 HIS   0.003   0.001   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9631)
  covalent geometry    : angle       0.62764 (13119)
  SS BOND              : bond        0.00465 (    4)
  SS BOND              : angle       3.33903 (    8)
  hydrogen bonds       : bond        0.03823 (  418)
  hydrogen bonds       : angle       4.71340 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 186
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.5370 (ttp)
REVERT: B  106 TRP cc_start: 0.8511 (m-10) cc_final: 0.8191 (m-90)
REVERT: B  187 MET cc_start: 0.8123 (tpp) cc_final: 0.7836 (tpp)
REVERT: B  215 MET cc_start: 0.8574 (tpp) cc_final: 0.8226 (tpp)
REVERT: B  311 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6622 (tt0)
REVERT: B  370 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7443 (tmmt)
REVERT: C  149 ILE cc_start: 0.8826 (mm) cc_final: 0.8563 (mt)
REVERT: C  176 GLN cc_start: 0.8248 (tt0) cc_final: 0.7878 (mt0)
REVERT: C  223 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7524 (ptt)
REVERT: C  257 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7843 (tt)
REVERT: D  111 MET cc_start: 0.6266 (tpt) cc_final: 0.6008 (tpp)
  outliers start: 41
  outliers final: 25
  residues processed: 212
  average time/residue: 0.0759
  time to fit residues: 24.6428
Evaluate side-chains
  206 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 177
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain C residue   94 ASN
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  223 MET
Chi-restraints excluded: chain C residue  257 LEU
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  247 LYS
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  304 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 52 optimal weight:    0.0770
   chunk 74 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 115 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 45 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0030
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.4148

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 ASN
B 176 GLN
** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 287 GLN
D  66 ASN
D 258 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.146136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.125662 restraints weight = 18856.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.127939 restraints weight = 13212.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.129456 restraints weight = 10400.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.130506 restraints weight = 8854.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.131283 restraints weight = 7916.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.4954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9635  Z= 0.121
  Angle     :  0.620   8.349  13127  Z= 0.321
  Chirality :  0.044   0.172   1557
  Planarity :  0.003   0.047   1640
  Dihedral  :  4.530  28.235   1323
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.52 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 22.76 %
    Favored  : 72.81 %
  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 are not related in a simple way.
  whole: -0.08 (0.24), residues: 1216
  helix:  1.93 (0.28), residues: 346
  sheet:  0.30 (0.35), residues: 233
  loop : -1.38 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 240 
 TYR   0.033   0.001   TYR A 157 
 PHE   0.019   0.001   PHE B 147 
 TRP   0.023   0.001   TRP C 106 
 HIS   0.002   0.001   HIS B 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 9631)
  covalent geometry    : angle       0.61566 (13119)
  SS BOND              : bond        0.00730 (    4)
  SS BOND              : angle       3.02986 (    8)
  hydrogen bonds       : bond        0.03566 (  418)
  hydrogen bonds       : angle       4.53916 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 178
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6205 (tpt) cc_final: 0.5452 (ttp)
REVERT: B  106 TRP cc_start: 0.8493 (m-10) cc_final: 0.8241 (m-90)
REVERT: B  215 MET cc_start: 0.8700 (tpp) cc_final: 0.8352 (tpp)
REVERT: B  236 GLU cc_start: 0.5235 (tp30) cc_final: 0.4681 (tp30)
REVERT: B  275 LEU cc_start: 0.5565 (pt) cc_final: 0.5357 (pt)
REVERT: B  370 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7381 (tmmt)
REVERT: C  111 MET cc_start: 0.7184 (tpp) cc_final: 0.6974 (tpp)
REVERT: C  134 CYS cc_start: 0.3871 (OUTLIER) cc_final: 0.3662 (p)
REVERT: C  149 ILE cc_start: 0.8855 (mm) cc_final: 0.8590 (mt)
REVERT: C  176 GLN cc_start: 0.8124 (tt0) cc_final: 0.7713 (mt0)
REVERT: C  187 MET cc_start: 0.8126 (tpt) cc_final: 0.7393 (tmm)
REVERT: C  223 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7457 (ptt)
REVERT: C  240 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7463 (mtm110)
REVERT: D  111 MET cc_start: 0.6298 (tpt) cc_final: 0.6047 (tpp)
REVERT: D  157 TYR cc_start: 0.6415 (m-80) cc_final: 0.6005 (m-10)
  outliers start: 43
  outliers final: 24
  residues processed: 204
  average time/residue: 0.0725
  time to fit residues: 23.0112
Evaluate side-chains
  195 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain C residue  134 CYS
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  223 MET
Chi-restraints excluded: chain C residue  240 ARG
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain D residue   66 ASN
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  258 ASN
Chi-restraints excluded: chain D residue  274 PHE
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  304 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 123 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 117 optimal weight:    8.9990
   chunk 75 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
B 176 GLN
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.143154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.122264 restraints weight = 19058.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.124481 restraints weight = 13581.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.125955 restraints weight = 10769.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.126724 restraints weight = 9218.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.127544 restraints weight = 8373.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.5078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9635  Z= 0.164
  Angle     :  0.649   7.961  13127  Z= 0.339
  Chirality :  0.044   0.178   1557
  Planarity :  0.004   0.046   1640
  Dihedral  :  4.685  24.577   1323
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.10 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 23.58 %
    Favored  : 72.09 %
  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 are not related in a simple way.
  whole: -0.12 (0.24), residues: 1216
  helix:  1.96 (0.28), residues: 343
  sheet:  0.18 (0.35), residues: 230
  loop : -1.39 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 240 
 TYR   0.028   0.001   TYR A 157 
 PHE   0.016   0.002   PHE B 147 
 TRP   0.028   0.002   TRP C 106 
 HIS   0.004   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9631)
  covalent geometry    : angle       0.64258 (13119)
  SS BOND              : bond        0.00517 (    4)
  SS BOND              : angle       3.67838 (    8)
  hydrogen bonds       : bond        0.03638 (  418)
  hydrogen bonds       : angle       4.61943 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 174
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5419 (ttp)
REVERT: B  106 TRP cc_start: 0.8523 (m-10) cc_final: 0.8198 (m-90)
REVERT: B  215 MET cc_start: 0.8678 (tpp) cc_final: 0.8327 (tpp)
REVERT: B  236 GLU cc_start: 0.5379 (tp30) cc_final: 0.5044 (tp30)
REVERT: B  370 LYS cc_start: 0.7724 (tmmt) cc_final: 0.7480 (tmmt)
REVERT: C  134 CYS cc_start: 0.4220 (OUTLIER) cc_final: 0.3971 (p)
REVERT: C  149 ILE cc_start: 0.8916 (mm) cc_final: 0.8608 (mt)
REVERT: C  176 GLN cc_start: 0.8166 (tt0) cc_final: 0.7833 (mt0)
REVERT: C  223 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7574 (ptt)
REVERT: D  111 MET cc_start: 0.6287 (tpt) cc_final: 0.6000 (tpp)
REVERT: D  157 TYR cc_start: 0.6869 (m-80) cc_final: 0.6666 (m-10)
REVERT: D  164 ASP cc_start: 0.8267 (p0) cc_final: 0.8049 (p0)
  outliers start: 42
  outliers final: 33
  residues processed: 201
  average time/residue: 0.0736
  time to fit residues: 23.0582
Evaluate side-chains
  205 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain C residue  134 CYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  223 MET
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  274 PHE
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  304 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 90 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 ASN
B 137 ASN
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 258 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 = 0.3894 r_free = 0.3894 target = 0.139612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.118191 restraints weight = 19048.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.120597 restraints weight = 13031.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.122204 restraints weight = 10094.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.123316 restraints weight = 8517.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.123929 restraints weight = 7572.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.5295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9635  Z= 0.240
  Angle     :  0.733   9.618  13127  Z= 0.389
  Chirality :  0.046   0.259   1557
  Planarity :  0.004   0.048   1640
  Dihedral  :  5.106  29.099   1323
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.18 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.48 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.24), residues: 1216
  helix:  1.85 (0.28), residues: 341
  sheet:  0.14 (0.35), residues: 222
  loop : -1.57 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 240 
 TYR   0.038   0.002   TYR A 157 
 PHE   0.022   0.002   PHE B 147 
 TRP   0.035   0.002   TRP C 106 
 HIS   0.006   0.002   HIS B 283 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 9631)
  covalent geometry    : angle       0.72773 (13119)
  SS BOND              : bond        0.00706 (    4)
  SS BOND              : angle       3.77435 (    8)
  hydrogen bonds       : bond        0.04038 (  418)
  hydrogen bonds       : angle       4.84955 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 167
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5423 (ttp)
REVERT: B  100 MET cc_start: 0.6659 (ptp) cc_final: 0.6374 (ptp)
REVERT: B  103 THR cc_start: 0.9098 (m) cc_final: 0.8666 (t)
REVERT: B  106 TRP cc_start: 0.8525 (m-10) cc_final: 0.8112 (m-90)
REVERT: B  137 ASN cc_start: 0.9064 (OUTLIER) cc_final: 0.8487 (t0)
REVERT: B  176 GLN cc_start: 0.8735 (tp40) cc_final: 0.8425 (mm110)
REVERT: B  213 ILE cc_start: 0.6996 (tt) cc_final: 0.6789 (tt)
REVERT: B  215 MET cc_start: 0.8763 (tpp) cc_final: 0.8364 (tpp)
REVERT: B  370 LYS cc_start: 0.7823 (tmmt) cc_final: 0.7562 (tmmt)
REVERT: C  149 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8671 (mt)
REVERT: C  176 GLN cc_start: 0.8144 (tt0) cc_final: 0.7810 (mt0)
REVERT: D  164 ASP cc_start: 0.8383 (p0) cc_final: 0.7794 (p0)
  outliers start: 47
  outliers final: 34
  residues processed: 195
  average time/residue: 0.0677
  time to fit residues: 20.2776
Evaluate side-chains
  202 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  223 MET
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  274 PHE
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  304 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 68 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 94 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
B 176 GLN
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.139946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.119073 restraints weight = 19003.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.121244 restraints weight = 13578.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.122648 restraints weight = 10798.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.123675 restraints weight = 9269.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.124371 restraints weight = 8306.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.5406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9635  Z= 0.216
  Angle     :  0.740  11.077  13127  Z= 0.389
  Chirality :  0.046   0.247   1557
  Planarity :  0.004   0.064   1640
  Dihedral  :  5.193  29.832   1323
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.35 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 24.41 %
    Favored  : 71.27 %
  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 are not related in a simple way.
  whole: -0.43 (0.24), residues: 1216
  helix:  1.79 (0.28), residues: 341
  sheet:  0.04 (0.36), residues: 222
  loop : -1.63 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 378 
 TYR   0.037   0.002   TYR A 157 
 PHE   0.026   0.002   PHE B 147 
 TRP   0.040   0.002   TRP C 106 
 HIS   0.006   0.002   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 9631)
  covalent geometry    : angle       0.72967 (13119)
  SS BOND              : bond        0.01094 (    4)
  SS BOND              : angle       4.98334 (    8)
  hydrogen bonds       : bond        0.04005 (  418)
  hydrogen bonds       : angle       4.89214 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.7467 (mtt) cc_final: 0.7202 (mtt)
REVERT: A  123 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5487 (ttp)
REVERT: B  106 TRP cc_start: 0.8506 (m-10) cc_final: 0.8123 (m-90)
REVERT: B  213 ILE cc_start: 0.6984 (tt) cc_final: 0.6783 (tt)
REVERT: B  215 MET cc_start: 0.8801 (tpp) cc_final: 0.8381 (tpp)
REVERT: B  236 GLU cc_start: 0.5098 (tp30) cc_final: 0.4500 (tp30)
REVERT: B  370 LYS cc_start: 0.7766 (tmmt) cc_final: 0.7537 (tmmt)
REVERT: C  149 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8636 (mt)
REVERT: C  176 GLN cc_start: 0.8061 (tt0) cc_final: 0.7768 (mt0)
REVERT: C  187 MET cc_start: 0.7935 (tpt) cc_final: 0.7279 (tmm)
REVERT: C  240 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7225 (mtm110)
REVERT: D  100 MET cc_start: 0.6974 (ptp) cc_final: 0.6519 (ptp)
REVERT: D  164 ASP cc_start: 0.8367 (p0) cc_final: 0.8046 (p0)
  outliers start: 42
  outliers final: 35
  residues processed: 188
  average time/residue: 0.0730
  time to fit residues: 20.9709
Evaluate side-chains
  194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 156
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  125 HIS
Chi-restraints excluded: chain A residue  137 ASN
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  325 SER
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  223 MET
Chi-restraints excluded: chain C residue  240 ARG
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  274 PHE
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  304 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 87 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 107 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 66 optimal weight:    0.5980
   chunk 112 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
B 176 GLN
** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 287 GLN
** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.146248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.126230 restraints weight = 19211.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.128329 restraints weight = 13867.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.129823 restraints weight = 11083.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.130823 restraints weight = 9475.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.131022 restraints weight = 8503.615|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.5584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9635  Z= 0.140
  Angle     :  0.685  11.014  13127  Z= 0.355
  Chirality :  0.045   0.260   1557
  Planarity :  0.004   0.054   1640
  Dihedral  :  4.753  26.877   1323
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.02 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 25.03 %
    Favored  : 71.06 %
  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 are not related in a simple way.
  whole: -0.17 (0.25), residues: 1216
  helix:  1.98 (0.28), residues: 341
  sheet:  0.31 (0.37), residues: 210
  loop : -1.46 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 378 
 TYR   0.026   0.001   TYR A 157 
 PHE   0.013   0.001   PHE A 254 
 TRP   0.039   0.002   TRP C 106 
 HIS   0.004   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9631)
  covalent geometry    : angle       0.67902 (13119)
  SS BOND              : bond        0.00222 (    4)
  SS BOND              : angle       3.60468 (    8)
  hydrogen bonds       : bond        0.03600 (  418)
  hydrogen bonds       : angle       4.64188 ( 1236)

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

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

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2432 Ramachandran restraints generated.
    1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 165
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.7452 (mtt) cc_final: 0.7219 (mtt)
REVERT: A  123 MET cc_start: 0.6249 (tpt) cc_final: 0.5393 (ttp)
REVERT: B  100 MET cc_start: 0.6658 (ptp) cc_final: 0.6400 (ptp)
REVERT: B  103 THR cc_start: 0.9085 (m) cc_final: 0.8659 (t)
REVERT: B  106 TRP cc_start: 0.8464 (m-10) cc_final: 0.8015 (m-90)
REVERT: B  213 ILE cc_start: 0.7139 (tt) cc_final: 0.6908 (tt)
REVERT: B  215 MET cc_start: 0.8766 (tpp) cc_final: 0.8334 (tpp)
REVERT: B  236 GLU cc_start: 0.4926 (tp30) cc_final: 0.4715 (tp30)
REVERT: B  370 LYS cc_start: 0.7722 (tmmt) cc_final: 0.7493 (tmmt)
REVERT: C  149 ILE cc_start: 0.8909 (mm) cc_final: 0.8653 (mt)
REVERT: C  176 GLN cc_start: 0.8022 (tt0) cc_final: 0.7075 (mt0)
REVERT: C  187 MET cc_start: 0.7946 (tpt) cc_final: 0.7375 (tmm)
REVERT: D  100 MET cc_start: 0.6899 (ptp) cc_final: 0.6497 (ptp)
REVERT: D  111 MET cc_start: 0.6218 (tpt) cc_final: 0.5972 (tpp)
REVERT: D  164 ASP cc_start: 0.8234 (p0) cc_final: 0.8005 (p0)
  outliers start: 38
  outliers final: 34
  residues processed: 188
  average time/residue: 0.0722
  time to fit residues: 21.2077
Evaluate side-chains
  193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  134 CYS
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  282 SER
Chi-restraints excluded: chain A residue  313 MET
Chi-restraints excluded: chain A residue  321 CYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  343 THR
Chi-restraints excluded: chain A residue  349 TYR
Chi-restraints excluded: chain B residue   65 CYS
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  137 ASN
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  221 CYS
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  192 PHE
Chi-restraints excluded: chain C residue  205 LEU
Chi-restraints excluded: chain C residue  223 MET
Chi-restraints excluded: chain C residue  283 HIS
Chi-restraints excluded: chain C residue  351 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  107 LEU
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  146 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain D residue  274 PHE
Chi-restraints excluded: chain D residue  282 SER
Chi-restraints excluded: chain D residue  304 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:   10.0000
   chunk 44 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 137 ASN
B 176 GLN
** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 258 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 = 0.3963 r_free = 0.3963 target = 0.146357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.125072 restraints weight = 19049.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.127534 restraints weight = 12768.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.129291 restraints weight = 9820.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.130063 restraints weight = 8207.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.131162 restraints weight = 7432.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.5605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.360   9635  Z= 0.381
  Angle     :  1.054  59.150  13127  Z= 0.665
  Chirality :  0.047   0.535   1557
  Planarity :  0.007   0.178   1640
  Dihedral  :  4.814  26.635   1323
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.26 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 25.44 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.17 %
  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 are not related in a simple way.
  whole: -0.25 (0.25), residues: 1216
  helix:  1.96 (0.28), residues: 341
  sheet:  0.15 (0.36), residues: 222
  loop : -1.52 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 240 
 TYR   0.024   0.001   TYR A 157 
 PHE   0.053   0.002   PHE C 109 
 TRP   0.036   0.002   TRP C 106 
 HIS   0.004   0.001   HIS B 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 ( 9631)
  covalent geometry    : angle       1.05054 (13119)
  SS BOND              : bond        0.00229 (    4)
  SS BOND              : angle       3.48562 (    8)
  hydrogen bonds       : bond        0.03791 (  418)
  hydrogen bonds       : angle       4.65624 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1629.92 seconds
wall clock time: 28 minutes 48.89 seconds (1728.89 seconds total)