Starting phenix.real_space_refine
on Sun May 11 05:16:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lx5_63466/05_2025/9lx5_63466.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lx5_63466/05_2025/9lx5_63466.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lx5_63466/05_2025/9lx5_63466.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lx5_63466/05_2025/9lx5_63466.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lx5_63466/05_2025/9lx5_63466.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lx5_63466/05_2025/9lx5_63466.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      40      5.16       5
     C    4829      2.51       5
     N    1293      2.21       5
     O    1348      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7519
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2452
          Classifications: {'peptide': 328}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 15, 'TRANS': 312}
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 173
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 73
    Chain: "B"
      Number of atoms: 2429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2429
          Classifications: {'peptide': 324}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 15, 'TRANS': 308}
          Unresolved non-hydrogen bonds: 133
          Unresolved non-hydrogen angles: 167
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 63
    Chain: "C"
      Number of atoms: 2461
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2461
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 15, 'TRANS': 313}
          Unresolved non-hydrogen bonds: 139
          Unresolved non-hydrogen angles: 177
          Unresolved non-hydrogen dihedrals: 112
          Unresolved non-hydrogen chiralities: 19
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "A"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 59
          Unusual residues: {'ATP': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 59
          Unusual residues: {'ATP': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 59
          Unusual residues: {'ATP': 1, 'CLR': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.28, per 1000 atoms: 0.70
  Number of scatterers: 7519
  At special positions: 0
  Unit cell: (85.68, 88.893, 122.094, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P       9     15.00
     O    1348      8.00
     N    1293      7.00
     C    4829      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 132 " - pdb=" SG  CYS A 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 217 " - pdb=" SG  CYS A 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 261 " - pdb=" SG  CYS A 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 165 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 132 " - pdb=" SG  CYS B 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 217 " - pdb=" SG  CYS B 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 261 " - pdb=" SG  CYS B 270 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 117 " - pdb=" SG  CYS C 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 126 " - pdb=" SG  CYS C 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 132 " - pdb=" SG  CYS C 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 217 " - pdb=" SG  CYS C 227 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 261 " - pdb=" SG  CYS C 270 " 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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.96
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1778

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 16 sheets defined
      23.9% alpha, 27.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 50
    Processing helix  chain 'A' and resid 51 through 53
      No H-bonds generated for 'chain 'A' and resid 51 through 53'
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.709A  pdb=" N   TYR A  90 " --> pdb=" O   ASP A  86 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL A  91 " --> pdb=" O   VAL A  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 86 through 91'
    Processing helix  chain 'A' and resid 179 through 184
      removed outlier: 3.600A  pdb=" N   ASN A 184 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 215
      removed outlier: 4.241A  pdb=" N   LYS A 215 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 239
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 327 through 355
      removed outlier: 3.584A  pdb=" N   THR A 331 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 52
      removed outlier: 3.782A  pdb=" N   GLU B  52 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
      removed outlier: 3.922A  pdb=" N   VAL B  91 " --> pdb=" O   VAL B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 124
    Processing helix  chain 'B' and resid 181 through 185
      removed outlier: 3.507A  pdb=" N   PHE B 185 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 237
      removed outlier: 3.521A  pdb=" N   VAL B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 250
      removed outlier: 4.269A  pdb=" N   LYS B 249 " --> pdb=" O   THR B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 354
      removed outlier: 3.574A  pdb=" N   THR B 331 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 51
    Processing helix  chain 'C' and resid 86 through 91
      removed outlier: 3.969A  pdb=" N   TYR C  90 " --> pdb=" O   ASP C  86 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   VAL C  91 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 86 through 91'
    Processing helix  chain 'C' and resid 210 through 215
    Processing helix  chain 'C' and resid 242 through 247
    Processing helix  chain 'C' and resid 327 through 357
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 67
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 67
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105
      removed outlier: 6.734A  pdb=" N   PHE A 311 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ASP A 320 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   CYS A 261 " --> pdb=" O   LYS A 322 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLY A 324 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 109
      removed outlier: 3.888A  pdb=" N   LEU A 307 " --> pdb=" O   THR A 109 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE A 297 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 114 through 118
      removed outlier: 3.757A  pdb=" N   GLY A 163 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   THR A 158 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LYS A 148 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   GLU A 160 " --> pdb=" O   THR A 146 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 63 through 64
      removed outlier: 3.505A  pdb=" N   SER B  64 " --> pdb=" O   SER B 192 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 75
      removed outlier: 3.622A  pdb=" N   THR B  75 " --> pdb=" O   GLN B  83 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   GLN B  83 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 102
    Processing sheet with id=AA9, first strand: chain 'B' and resid 115 through 118
    Processing sheet with id=AB1, first strand: chain 'B' and resid 290 through 298
      removed outlier: 3.824A  pdb=" N   PHE B 297 " --> pdb=" O   TYR B 304 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 62 through 64
    Processing sheet with id=AB3, first strand: chain 'C' and resid 67 through 70
    Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 75
      removed outlier: 3.546A  pdb=" N   ALA C  73 " --> pdb=" O   TRP C  85 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 105
      removed outlier: 3.574A  pdb=" N   PHE C 100 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   PHE C 311 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   GLY C 254 " --> pdb=" O   HIS C 277 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 108 through 112
      removed outlier: 3.691A  pdb=" N   LEU C 307 " --> pdb=" O   THR C 109 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS C 111 " --> pdb=" O   ARG C 305 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ARG C 305 " --> pdb=" O   LYS C 111 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 114 through 118
      removed outlier: 5.467A  pdb=" N   LYS C 148 " --> pdb=" O   GLU C 160 " (cutoff:3.500A)
      removed outlier: 8.652A  pdb=" N   PHE C 162 " --> pdb=" O   THR C 146 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   THR C 146 " --> pdb=" O   PHE C 162 " (cutoff:3.500A)
      removed outlier: 9.069A  pdb=" N   TRP C 164 " --> pdb=" O   ILE C 144 " (cutoff:3.500A)
      removed outlier: 8.833A  pdb=" N   ILE C 144 " --> pdb=" O   TRP C 164 " (cutoff:3.500A)

    271 hydrogen bonds defined for protein.
    723 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: 1.82

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2423
        1.34 -     1.46: 1864
        1.46 -     1.58: 3378
        1.58 -     1.70: 10
        1.70 -     1.82: 49
  Bond restraints: 7724
  Sorted by residual:
  bond pdb=" C   ARG A 175 "
       pdb=" N   PRO A 176 "
    ideal  model  delta    sigma   weight residual
    1.337  1.350 -0.013 9.80e-03 1.04e+04 1.80e+00
  bond pdb=" C   CYS B 165 "
       pdb=" N   PRO B 166 "
    ideal  model  delta    sigma   weight residual
    1.334  1.365 -0.031 2.34e-02 1.83e+03 1.74e+00
  bond pdb=" CA  PHE B 311 "
       pdb=" CB  PHE B 311 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 1.47e-02 4.63e+03 1.68e+00
  bond pdb=" CG1 ILE A 193 "
       pdb=" CD1 ILE A 193 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.25e+00
  bond pdb=" C   GLY B  81 "
       pdb=" N   PRO B  82 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 8.64e-01
  ... (remaining 7719 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 10259
        1.54 -     3.08: 245
        3.08 -     4.62: 44
        4.62 -     6.16: 9
        6.16 -     7.70: 2
  Bond angle restraints: 10559
  Sorted by residual:
  angle pdb=" C   PHE C  92 "
        pdb=" N   PRO C  93 "
        pdb=" CA  PRO C  93 "
      ideal   model   delta    sigma   weight residual
     119.84  115.95    3.89 1.25e+00 6.40e-01 9.71e+00
  angle pdb=" C   ASN C 153 "
        pdb=" CA  ASN C 153 "
        pdb=" CB  ASN C 153 "
      ideal   model   delta    sigma   weight residual
     110.42  115.92   -5.50 1.99e+00 2.53e-01 7.64e+00
  angle pdb=" N   TYR A  55 "
        pdb=" CA  TYR A  55 "
        pdb=" CB  TYR A  55 "
      ideal   model   delta    sigma   weight residual
     113.65  109.89    3.76 1.47e+00 4.63e-01 6.55e+00
  angle pdb=" N   GLY A 288 "
        pdb=" CA  GLY A 288 "
        pdb=" C   GLY A 288 "
      ideal   model   delta    sigma   weight residual
     112.18  115.49   -3.31 1.34e+00 5.57e-01 6.11e+00
  angle pdb=" C   GLU B 207 "
        pdb=" N   GLU B 208 "
        pdb=" CA  GLU B 208 "
      ideal   model   delta    sigma   weight residual
     121.54  126.19   -4.65 1.91e+00 2.74e-01 5.93e+00
  ... (remaining 10554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 3894
       17.12 -    34.24: 534
       34.24 -    51.35: 208
       51.35 -    68.47: 38
       68.47 -    85.59: 12
  Dihedral angle restraints: 4686
    sinusoidal: 1907
      harmonic: 2779
  Sorted by residual:
  dihedral pdb=" CB  CYS A 117 "
           pdb=" SG  CYS A 117 "
           pdb=" SG  CYS A 165 "
           pdb=" CB  CYS A 165 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.92  -83.92     1      1.00e+01 1.00e-02 8.58e+01
  dihedral pdb=" CB  CYS C 126 "
           pdb=" SG  CYS C 126 "
           pdb=" SG  CYS C 149 "
           pdb=" CB  CYS C 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.46   82.46     1      1.00e+01 1.00e-02 8.34e+01
  dihedral pdb=" CB  CYS B 126 "
           pdb=" SG  CYS B 126 "
           pdb=" SG  CYS B 149 "
           pdb=" CB  CYS B 149 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -134.76   48.76     1      1.00e+01 1.00e-02 3.27e+01
  ... (remaining 4683 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 723
       0.036 -    0.071: 307
       0.071 -    0.107: 112
       0.107 -    0.143: 36
       0.143 -    0.178: 9
  Chirality restraints: 1187
  Sorted by residual:
  chirality pdb=" C20 CLR B 401 "
            pdb=" C17 CLR B 401 "
            pdb=" C21 CLR B 401 "
            pdb=" C22 CLR B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.41    0.18 2.00e-01 2.50e+01 7.94e-01
  chirality pdb=" CA  PHE B  92 "
            pdb=" N   PHE B  92 "
            pdb=" C   PHE B  92 "
            pdb=" CB  PHE B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CB  ILE C  45 "
            pdb=" CA  ILE C  45 "
            pdb=" CG1 ILE C  45 "
            pdb=" CG2 ILE C  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.46e-01
  ... (remaining 1184 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  81 "    0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO B  82 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B  82 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  82 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 120 "    0.028 5.00e-02 4.00e+02   4.24e-02 2.88e+00
        pdb=" N   PRO A 121 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 121 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 121 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 155 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   THR A 155 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   THR A 155 "    0.009 2.00e-02 2.50e+03
        pdb=" N   VAL A 156 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1307
        2.76 -     3.30: 6807
        3.30 -     3.83: 11732
        3.83 -     4.37: 12949
        4.37 -     4.90: 23614
  Nonbonded interactions: 56409
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 112 "
            pdb=" O   VAL B 167 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" O   GLY A 250 "
            pdb=" N   PHE A 289 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   CYS A 217 "
            pdb=" NH1 ARG B 139 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O   THR B 216 "
            pdb=" OG1 THR B 216 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG1 THR C 186 "
            pdb=" N6  ATP C 401 "
     model   vdw
     2.262 2.496
  ... (remaining 56404 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 31 through 43 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 44 through 51 or (resid 52 through 53 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 54 through 157 or (resid 158 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 159 through 166 or \ 
 (resid 167 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 
8 through 198 or (resid 199 and (name N or name CA or name C or name O or name C \ 
B )) or resid 200 through 205 or (resid 206 through 208 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 209 through 233 or (resid 234 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 235 through 245 or (re \ 
sid 246 through 247 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 248 through 265 or (resid 266 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 267 through 274 or (resid 275 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 276 through 325 or (resid 326 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 327 through 345 or (resid  \ 
346 and (name N or name CA or name C or name O or name CB )) or resid 347 throug \ 
h 348 or (resid 349 through 354 and (name N or name CA or name C or name O or na \ 
me CB ))))
  selection = (chain 'B' and ((resid 31 through 43 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 44 through 51 or (resid 52 through 53 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 54 through 118 or (resid 119 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 120 through 128 or \ 
 (resid 129 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 
0 through 132 or (resid 133 and (name N or name CA or name C or name O or name C \ 
B )) or resid 134 through 157 or (resid 158 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 159 or (resid 160 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 161 through 174 or (resid 175 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 176 through 214 or (resid 215  \ 
and (name N or name CA or name C or name O or name CB )) or resid 216 through 23 \ 
3 or (resid 234 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 235 through 245 or (resid 246 through 247 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 248 through 284 or (resid 285 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 286 through 325 or (resid 326 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 327 through 354))
  selection = (chain 'C' and ((resid 31 through 43 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 44 through 52 or (resid 53 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 54 through 118 or (resid 119 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 120 through 128 or (resid 129 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 130 through 1 \ 
32 or (resid 133 and (name N or name CA or name C or name O or name CB )) or res \ 
id 134 through 159 or (resid 160 and (name N or name CA or name C or name O or n \ 
ame CB )) or resid 161 through 166 or (resid 167 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 168 through 174 or (resid 175 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 176 through 198 or (resid 199 \ 
 and (name N or name CA or name C or name O or name CB )) or resid 200 through 2 \ 
05 or (resid 206 through 208 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 209 through 214 or (resid 215 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 216 through 265 or (resid 266 and (name N or name \ 
 CA or name C or name O or name CB )) or resid 267 through 274 or (resid 275 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 276 through 279 o \ 
r (resid 280 through 283 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 284 or (resid 285 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 286 through 345 or (resid 346 and (name N or name CA or name C or \ 
 name O or name CB )) or resid 347 through 354))
}

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:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.520
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
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      :  0.004   0.044   7741  Z= 0.155
  Angle     :  0.590   7.697  10589  Z= 0.316
  Chirality :  0.048   0.178   1187
  Planarity :  0.004   0.043   1336
  Dihedral  : 17.832  85.590   2863
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.38 %
    Favored  : 88.62 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 36.05 %
    Favored  : 59.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.29), residues: 975
  helix:  2.70 (0.40), residues: 187
  sheet: -0.61 (0.34), residues: 288
  loop : -2.87 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 259 
 HIS   0.007   0.001   HIS B 120 
 PHE   0.014   0.002   PHE A 195 
 TYR   0.010   0.001   TYR A  90 
 ARG   0.003   0.000   ARG C 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13892 (  265)
  hydrogen bonds       : angle       5.93580 (  723)
  SS BOND              : bond        0.00371 (   15)
  SS BOND              : angle       1.15367 (   30)
  covalent geometry    : bond        0.00351 ( 7724)
  covalent geometry    : angle       0.58784 (10559)
  Misc. bond           : bond        0.00061 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A   97 ASP cc_start: 0.8839 (t0) cc_final: 0.8566 (t0)
REVERT: B   52 GLU cc_start: 0.8338 (pt0) cc_final: 0.7717 (pm20)
REVERT: B  193 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7394 (mp)
REVERT: B  279 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7259 (tt)
REVERT: B  322 LYS cc_start: 0.7391 (mmmm) cc_final: 0.6070 (pttt)
REVERT: C  172 ASP cc_start: 0.8091 (m-30) cc_final: 0.7027 (p0)
REVERT: C  216 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7906 (t)
REVERT: C  265 TRP cc_start: 0.8808 (m-10) cc_final: 0.8306 (m-10)
REVERT: C  280 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4686 (m-80)
  outliers start: 31
  outliers final: 23
  residues processed: 110
  average time/residue: 0.1520
  time to fit residues: 24.2795
Evaluate side-chains
  110 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 83
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  271 ARG
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    0.1980
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 75 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0470
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.4678

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

Flipped N/Q/H residues before XYZ refinement:
B 284 ASN
C  76 GLN
C 204 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.160812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.122478 restraints weight = 9292.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.124281 restraints weight = 7307.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.125328 restraints weight = 6264.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.0559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7741  Z= 0.121
  Angle     :  0.547   5.911  10589  Z= 0.291
  Chirality :  0.047   0.178   1187
  Planarity :  0.004   0.045   1336
  Dihedral  : 10.189  71.357   1382
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  8.44 %
    Allowed  : 31.29 %
    Favored  : 60.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.29), residues: 975
  helix:  2.64 (0.40), residues: 188
  sheet: -0.69 (0.35), residues: 267
  loop : -2.85 (0.26), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  85 
 HIS   0.003   0.001   HIS B 120 
 PHE   0.013   0.001   PHE A  92 
 TYR   0.017   0.001   TYR B  90 
 ARG   0.002   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02809 (  265)
  hydrogen bonds       : angle       4.84910 (  723)
  SS BOND              : bond        0.00247 (   15)
  SS BOND              : angle       0.75975 (   30)
  covalent geometry    : bond        0.00272 ( 7724)
  covalent geometry    : angle       0.54674 (10559)
  Misc. bond           : bond        0.00135 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 95
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   97 ASP cc_start: 0.8800 (t0) cc_final: 0.8414 (t0)
REVERT: A  180 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6130 (ptp90)
REVERT: B   52 GLU cc_start: 0.8309 (pt0) cc_final: 0.7619 (pm20)
REVERT: B  184 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7653 (m110)
REVERT: B  193 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7593 (mp)
REVERT: B  213 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6340 (t-170)
REVERT: B  309 LYS cc_start: 0.8702 (tttt) cc_final: 0.8262 (tttp)
REVERT: B  322 LYS cc_start: 0.7051 (mmmm) cc_final: 0.5708 (pttt)
REVERT: C   69 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8307 (mp)
REVERT: C  129 ASP cc_start: 0.8514 (t0) cc_final: 0.8188 (t70)
REVERT: C  172 ASP cc_start: 0.8163 (m-30) cc_final: 0.7042 (p0)
REVERT: C  216 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7562 (t)
REVERT: C  265 TRP cc_start: 0.8807 (m-10) cc_final: 0.8315 (m-10)
REVERT: C  280 TYR cc_start: 0.6087 (OUTLIER) cc_final: 0.4686 (m-80)
  outliers start: 62
  outliers final: 35
  residues processed: 144
  average time/residue: 0.1471
  time to fit residues: 31.1200
Evaluate side-chains
  132 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 90
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  207 GLU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  213 HIS
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 64 optimal weight:   70.0000
   chunk 30 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 56 optimal weight:    0.4980
   chunk 78 optimal weight:    7.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
C  76 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.158533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.117627 restraints weight = 9461.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.120107 restraints weight = 6846.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.121494 restraints weight = 5541.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7741  Z= 0.147
  Angle     :  0.563   5.963  10589  Z= 0.299
  Chirality :  0.048   0.181   1187
  Planarity :  0.004   0.044   1336
  Dihedral  : 10.197  72.483   1375
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  8.98 %
    Allowed  : 30.48 %
    Favored  : 60.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.29), residues: 975
  helix:  2.75 (0.40), residues: 188
  sheet: -0.74 (0.33), residues: 288
  loop : -2.84 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  85 
 HIS   0.002   0.001   HIS A 277 
 PHE   0.013   0.001   PHE A  92 
 TYR   0.014   0.001   TYR B  90 
 ARG   0.002   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02590 (  265)
  hydrogen bonds       : angle       4.58177 (  723)
  SS BOND              : bond        0.00341 (   15)
  SS BOND              : angle       0.90219 (   30)
  covalent geometry    : bond        0.00343 ( 7724)
  covalent geometry    : angle       0.56154 (10559)
  Misc. bond           : bond        0.00154 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 89
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 ASP cc_start: 0.8879 (t0) cc_final: 0.8649 (t0)
REVERT: A  136 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7597 (mtpp)
REVERT: A  180 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6294 (ptp90)
REVERT: B   52 GLU cc_start: 0.8265 (pt0) cc_final: 0.7689 (pm20)
REVERT: B  184 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7723 (m110)
REVERT: B  279 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7093 (tt)
REVERT: B  322 LYS cc_start: 0.7454 (mmmm) cc_final: 0.6234 (pttt)
REVERT: C   47 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.6699 (t-100)
REVERT: C   69 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8338 (mp)
REVERT: C  103 MET cc_start: 0.8255 (ttp) cc_final: 0.8006 (ttm)
REVERT: C  172 ASP cc_start: 0.8125 (m-30) cc_final: 0.7021 (p0)
REVERT: C  216 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7693 (t)
REVERT: C  265 TRP cc_start: 0.8793 (m-10) cc_final: 0.8308 (m-10)
REVERT: C  280 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.4754 (m-80)
REVERT: C  327 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6978 (t70)
  outliers start: 66
  outliers final: 41
  residues processed: 143
  average time/residue: 0.1445
  time to fit residues: 30.3192
Evaluate side-chains
  133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 83
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue   95 GLN
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  327 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 204 ASN
B 269 HIS
B 303 ASN
C  76 GLN
C 277 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.156483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.117138 restraints weight = 9415.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.119172 restraints weight = 7159.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.120285 restraints weight = 5980.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.0988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7741  Z= 0.174
  Angle     :  0.588   6.117  10589  Z= 0.312
  Chirality :  0.049   0.202   1187
  Planarity :  0.004   0.046   1336
  Dihedral  : 10.353  73.784   1371
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.49 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  9.80 %
    Allowed  : 28.98 %
    Favored  : 61.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.29), residues: 975
  helix:  2.29 (0.40), residues: 200
  sheet: -0.81 (0.33), residues: 289
  loop : -2.90 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  85 
 HIS   0.008   0.001   HIS B 269 
 PHE   0.015   0.002   PHE A  92 
 TYR   0.013   0.001   TYR A  55 
 ARG   0.003   0.000   ARG B 268 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02610 (  265)
  hydrogen bonds       : angle       4.53894 (  723)
  SS BOND              : bond        0.00366 (   15)
  SS BOND              : angle       0.93658 (   30)
  covalent geometry    : bond        0.00411 ( 7724)
  covalent geometry    : angle       0.58672 (10559)
  Misc. bond           : bond        0.00151 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 82
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7604 (mtpp)
REVERT: B   52 GLU cc_start: 0.8269 (pt0) cc_final: 0.7680 (pm20)
REVERT: B  184 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7799 (m110)
REVERT: B  213 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.6577 (t-170)
REVERT: B  279 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7301 (tt)
REVERT: B  322 LYS cc_start: 0.7557 (mmmm) cc_final: 0.6326 (pttt)
REVERT: C   47 TRP cc_start: 0.7143 (OUTLIER) cc_final: 0.6800 (t-100)
REVERT: C   69 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8337 (mp)
REVERT: C  103 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8069 (ttm)
REVERT: C  129 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8228 (t70)
REVERT: C  172 ASP cc_start: 0.8158 (m-30) cc_final: 0.6989 (p0)
REVERT: C  216 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7723 (t)
REVERT: C  265 TRP cc_start: 0.8782 (m-10) cc_final: 0.8274 (m-10)
REVERT: C  280 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.4779 (m-80)
REVERT: C  305 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.8959 (ptt180)
REVERT: C  327 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6920 (t70)
  outliers start: 72
  outliers final: 42
  residues processed: 143
  average time/residue: 0.1523
  time to fit residues: 31.4744
Evaluate side-chains
  137 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 83
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   95 GLN
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  213 HIS
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  142 GLN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  285 LEU
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  305 ARG
Chi-restraints excluded: chain C residue  327 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0270
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.158670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.120744 restraints weight = 9349.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.120579 restraints weight = 7549.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.123202 restraints weight = 7072.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7741  Z= 0.130
  Angle     :  0.563   7.134  10589  Z= 0.297
  Chirality :  0.048   0.181   1187
  Planarity :  0.004   0.045   1336
  Dihedral  : 10.278  74.485   1371
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  9.12 %
    Allowed  : 30.07 %
    Favored  : 60.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.29), residues: 975
  helix:  2.54 (0.40), residues: 194
  sheet: -0.77 (0.33), residues: 288
  loop : -2.88 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  85 
 HIS   0.003   0.000   HIS A 277 
 PHE   0.018   0.001   PHE A  92 
 TYR   0.015   0.001   TYR B  90 
 ARG   0.002   0.000   ARG A 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02423 (  265)
  hydrogen bonds       : angle       4.44052 (  723)
  SS BOND              : bond        0.00303 (   15)
  SS BOND              : angle       0.81337 (   30)
  covalent geometry    : bond        0.00301 ( 7724)
  covalent geometry    : angle       0.56173 (10559)
  Misc. bond           : bond        0.00133 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 86
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7497 (mtpp)
REVERT: A  152 PHE cc_start: 0.6201 (t80) cc_final: 0.5869 (t80)
REVERT: B   52 GLU cc_start: 0.8270 (pt0) cc_final: 0.7634 (pm20)
REVERT: B  279 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7138 (tt)
REVERT: B  309 LYS cc_start: 0.8770 (tttt) cc_final: 0.8484 (tttp)
REVERT: B  322 LYS cc_start: 0.7390 (mmmm) cc_final: 0.6162 (pttt)
REVERT: C   47 TRP cc_start: 0.6987 (OUTLIER) cc_final: 0.6643 (t-100)
REVERT: C   69 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8413 (mp)
REVERT: C  103 MET cc_start: 0.8283 (ttp) cc_final: 0.8044 (ttm)
REVERT: C  129 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8180 (t70)
REVERT: C  172 ASP cc_start: 0.8128 (m-30) cc_final: 0.6983 (p0)
REVERT: C  216 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7629 (t)
REVERT: C  265 TRP cc_start: 0.8797 (m-10) cc_final: 0.8300 (m-10)
REVERT: C  280 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.4709 (m-80)
REVERT: C  327 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6888 (t70)
  outliers start: 67
  outliers final: 45
  residues processed: 143
  average time/residue: 0.1338
  time to fit residues: 28.7837
Evaluate side-chains
  134 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 81
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue   95 GLN
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  142 GLN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  327 ASP
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 32 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 26 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B 184 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.160202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.121798 restraints weight = 9448.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.121732 restraints weight = 7616.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.123694 restraints weight = 7324.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7741  Z= 0.121
  Angle     :  0.560  10.771  10589  Z= 0.293
  Chirality :  0.048   0.192   1187
  Planarity :  0.004   0.045   1336
  Dihedral  : 10.207  73.649   1371
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  8.03 %
    Allowed  : 30.88 %
    Favored  : 61.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.29), residues: 975
  helix:  2.17 (0.39), residues: 206
  sheet: -0.67 (0.33), residues: 287
  loop : -2.82 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  85 
 HIS   0.003   0.000   HIS A 277 
 PHE   0.024   0.001   PHE C 152 
 TYR   0.017   0.001   TYR B  90 
 ARG   0.001   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02315 (  265)
  hydrogen bonds       : angle       4.32019 (  723)
  SS BOND              : bond        0.00276 (   15)
  SS BOND              : angle       0.88900 (   30)
  covalent geometry    : bond        0.00279 ( 7724)
  covalent geometry    : angle       0.55869 (10559)
  Misc. bond           : bond        0.00127 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 87
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7510 (mtpp)
REVERT: B   52 GLU cc_start: 0.8273 (pt0) cc_final: 0.7626 (pm20)
REVERT: B  279 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7143 (tt)
REVERT: B  309 LYS cc_start: 0.8793 (tttt) cc_final: 0.8479 (tttp)
REVERT: B  322 LYS cc_start: 0.7347 (mmmm) cc_final: 0.6127 (pttt)
REVERT: C   47 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.6564 (t-100)
REVERT: C   69 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8387 (mp)
REVERT: C  103 MET cc_start: 0.8260 (ttp) cc_final: 0.8041 (ttm)
REVERT: C  172 ASP cc_start: 0.8126 (m-30) cc_final: 0.6954 (p0)
REVERT: C  216 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7601 (t)
REVERT: C  265 TRP cc_start: 0.8791 (m-10) cc_final: 0.8307 (m-10)
REVERT: C  280 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.4670 (m-80)
REVERT: C  305 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.8976 (ptt180)
REVERT: C  327 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6873 (t0)
  outliers start: 59
  outliers final: 42
  residues processed: 136
  average time/residue: 0.1425
  time to fit residues: 28.6358
Evaluate side-chains
  135 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 85
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  117 CYS
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  305 ARG
Chi-restraints excluded: chain C residue  327 ASP
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 74 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0370
   chunk 43 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.160929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.121750 restraints weight = 9310.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.123964 restraints weight = 6901.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.125533 restraints weight = 5692.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7741  Z= 0.125
  Angle     :  0.560   8.887  10589  Z= 0.294
  Chirality :  0.048   0.181   1187
  Planarity :  0.004   0.045   1336
  Dihedral  : 10.188  73.415   1371
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 30.48 %
    Favored  : 61.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.29), residues: 975
  helix:  2.18 (0.39), residues: 206
  sheet: -0.64 (0.34), residues: 288
  loop : -2.80 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  85 
 HIS   0.003   0.000   HIS A 277 
 PHE   0.022   0.001   PHE C 152 
 TYR   0.017   0.001   TYR B  90 
 ARG   0.001   0.000   ARG B 139 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02294 (  265)
  hydrogen bonds       : angle       4.28488 (  723)
  SS BOND              : bond        0.00301 (   15)
  SS BOND              : angle       0.85474 (   30)
  covalent geometry    : bond        0.00289 ( 7724)
  covalent geometry    : angle       0.55888 (10559)
  Misc. bond           : bond        0.00125 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 88
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7575 (mtpp)
REVERT: B   52 GLU cc_start: 0.8243 (pt0) cc_final: 0.7663 (pm20)
REVERT: B  213 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.6620 (t-170)
REVERT: B  279 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7150 (tt)
REVERT: B  309 LYS cc_start: 0.8792 (tttt) cc_final: 0.8486 (tttp)
REVERT: B  322 LYS cc_start: 0.7409 (mmmm) cc_final: 0.6167 (pttt)
REVERT: C   47 TRP cc_start: 0.7089 (OUTLIER) cc_final: 0.6766 (t-100)
REVERT: C   69 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8396 (mp)
REVERT: C  103 MET cc_start: 0.8233 (ttp) cc_final: 0.8001 (ttm)
REVERT: C  172 ASP cc_start: 0.8131 (m-30) cc_final: 0.6955 (p0)
REVERT: C  216 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7599 (t)
REVERT: C  265 TRP cc_start: 0.8794 (m-10) cc_final: 0.8312 (m-10)
REVERT: C  280 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.4655 (m-80)
REVERT: C  305 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8982 (ptt180)
  outliers start: 60
  outliers final: 45
  residues processed: 138
  average time/residue: 0.1537
  time to fit residues: 30.7373
Evaluate side-chains
  133 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 80
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  117 CYS
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  213 HIS
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  142 GLN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  305 ARG
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 75 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:   20.0000
   chunk 90 optimal weight:    0.6980
   overall best weight:    1.2382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.155182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.114345 restraints weight = 9512.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.116746 restraints weight = 6897.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.118403 restraints weight = 5616.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   7741  Z= 0.194
  Angle     :  0.623   8.088  10589  Z= 0.329
  Chirality :  0.051   0.224   1187
  Planarity :  0.004   0.047   1336
  Dihedral  : 10.531  75.223   1371
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.21 %
    Favored  : 87.79 %
  Rotamer:
    Outliers :  8.44 %
    Allowed  : 29.93 %
    Favored  : 61.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.29), residues: 975
  helix:  2.11 (0.39), residues: 206
  sheet: -0.77 (0.34), residues: 281
  loop : -2.84 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  85 
 HIS   0.005   0.001   HIS B 120 
 PHE   0.024   0.002   PHE C 152 
 TYR   0.014   0.001   TYR A  55 
 ARG   0.002   0.000   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02558 (  265)
  hydrogen bonds       : angle       4.42727 (  723)
  SS BOND              : bond        0.00394 (   15)
  SS BOND              : angle       1.01549 (   30)
  covalent geometry    : bond        0.00462 ( 7724)
  covalent geometry    : angle       0.62134 (10559)
  Misc. bond           : bond        0.00154 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 83
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7568 (mtpp)
REVERT: B   52 GLU cc_start: 0.8228 (pt0) cc_final: 0.7635 (pm20)
REVERT: B  213 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6681 (t-170)
REVERT: B  279 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7285 (tt)
REVERT: B  322 LYS cc_start: 0.7739 (mmmm) cc_final: 0.6528 (pttt)
REVERT: C   47 TRP cc_start: 0.7170 (OUTLIER) cc_final: 0.6809 (t-100)
REVERT: C   69 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8323 (mp)
REVERT: C  103 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8094 (ttm)
REVERT: C  129 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8212 (t70)
REVERT: C  216 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7658 (t)
REVERT: C  265 TRP cc_start: 0.8786 (m-10) cc_final: 0.8262 (m-10)
REVERT: C  280 TYR cc_start: 0.6386 (OUTLIER) cc_final: 0.4872 (m-80)
REVERT: C  305 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.8979 (ptt180)
  outliers start: 62
  outliers final: 44
  residues processed: 131
  average time/residue: 0.1395
  time to fit residues: 27.1754
Evaluate side-chains
  135 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 81
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  117 CYS
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   95 GLN
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  213 HIS
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  142 GLN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  305 ARG
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    0.0040
   chunk 95 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 75 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.156307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.119924 restraints weight = 9550.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.117253 restraints weight = 8347.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.118799 restraints weight = 8077.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7741  Z= 0.149
  Angle     :  0.592   7.971  10589  Z= 0.312
  Chirality :  0.049   0.184   1187
  Planarity :  0.004   0.046   1336
  Dihedral  : 10.460  76.330   1371
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  8.71 %
    Allowed  : 30.20 %
    Favored  : 61.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.28), residues: 975
  helix:  2.05 (0.39), residues: 206
  sheet: -0.81 (0.33), residues: 288
  loop : -2.90 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  85 
 HIS   0.006   0.001   HIS B 120 
 PHE   0.028   0.002   PHE C 152 
 TYR   0.016   0.001   TYR B  90 
 ARG   0.002   0.000   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02415 (  265)
  hydrogen bonds       : angle       4.39603 (  723)
  SS BOND              : bond        0.00338 (   15)
  SS BOND              : angle       0.99165 (   30)
  covalent geometry    : bond        0.00350 ( 7724)
  covalent geometry    : angle       0.59043 (10559)
  Misc. bond           : bond        0.00143 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 79
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7532 (mtpp)
REVERT: B   52 GLU cc_start: 0.8218 (pt0) cc_final: 0.7593 (pm20)
REVERT: B  213 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6578 (t-170)
REVERT: B  279 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7290 (tt)
REVERT: B  309 LYS cc_start: 0.8874 (tttt) cc_final: 0.8470 (tttp)
REVERT: B  322 LYS cc_start: 0.7535 (mmmm) cc_final: 0.6321 (pttt)
REVERT: C   47 TRP cc_start: 0.7209 (OUTLIER) cc_final: 0.6879 (t-100)
REVERT: C   69 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8360 (mp)
REVERT: C  103 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8054 (ttm)
REVERT: C  129 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8200 (t70)
REVERT: C  150 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8651 (m)
REVERT: C  216 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7498 (t)
REVERT: C  265 TRP cc_start: 0.8774 (m-10) cc_final: 0.8265 (m-10)
REVERT: C  280 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.4859 (m-80)
REVERT: C  305 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9012 (ptt180)
  outliers start: 64
  outliers final: 49
  residues processed: 130
  average time/residue: 0.1441
  time to fit residues: 27.7507
Evaluate side-chains
  138 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 78
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  117 CYS
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  213 HIS
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  306 HIS
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  142 GLN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  305 ARG
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 2 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.155132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.118450 restraints weight = 9446.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.116436 restraints weight = 8765.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.117962 restraints weight = 7938.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7741  Z= 0.186
  Angle     :  0.632  10.821  10589  Z= 0.330
  Chirality :  0.051   0.220   1187
  Planarity :  0.004   0.047   1336
  Dihedral  : 10.533  77.415   1369
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.51 %
    Favored  : 87.49 %
  Rotamer:
    Outliers :  8.16 %
    Allowed  : 30.75 %
    Favored  : 61.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.28), residues: 975
  helix:  1.75 (0.39), residues: 213
  sheet: -0.90 (0.33), residues: 289
  loop : -2.96 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  85 
 HIS   0.005   0.001   HIS B 120 
 PHE   0.029   0.002   PHE C 152 
 TYR   0.014   0.001   TYR A  55 
 ARG   0.002   0.000   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02581 (  265)
  hydrogen bonds       : angle       4.48387 (  723)
  SS BOND              : bond        0.00395 (   15)
  SS BOND              : angle       1.20288 (   30)
  covalent geometry    : bond        0.00443 ( 7724)
  covalent geometry    : angle       0.62986 (10559)
  Misc. bond           : bond        0.00153 (    2)

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

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

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1950 Ramachandran restraints generated.
    975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 84
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7473 (mtpp)
REVERT: B   52 GLU cc_start: 0.8277 (pt0) cc_final: 0.7597 (pm20)
REVERT: B  213 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6575 (t-170)
REVERT: B  279 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7263 (tt)
REVERT: B  309 LYS cc_start: 0.8910 (tttt) cc_final: 0.8625 (tttp)
REVERT: B  322 LYS cc_start: 0.7755 (mmmm) cc_final: 0.6579 (pttt)
REVERT: C   47 TRP cc_start: 0.7202 (OUTLIER) cc_final: 0.6885 (t-100)
REVERT: C   69 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8309 (mp)
REVERT: C  103 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8074 (ttm)
REVERT: C  129 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8245 (t70)
REVERT: C  150 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8635 (m)
REVERT: C  216 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7719 (t)
REVERT: C  265 TRP cc_start: 0.8748 (m-10) cc_final: 0.8460 (m-10)
REVERT: C  280 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.4935 (m-80)
REVERT: C  305 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.9001 (ptt180)
  outliers start: 60
  outliers final: 47
  residues processed: 133
  average time/residue: 0.1487
  time to fit residues: 28.8163
Evaluate side-chains
  136 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 78
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 TYR
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain A residue  117 CYS
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  136 LYS
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  335 ILE
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain B residue   47 TRP
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  104 THR
Chi-restraints excluded: chain B residue  165 CYS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  205 LEU
Chi-restraints excluded: chain B residue  213 HIS
Chi-restraints excluded: chain B residue  217 CYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  335 ILE
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   69 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  109 THR
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  142 GLN
Chi-restraints excluded: chain C residue  150 VAL
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  179 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  217 CYS
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  227 CYS
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  263 LEU
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  280 TYR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  305 ARG
Chi-restraints excluded: chain C residue  335 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.156338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.123266 restraints weight = 9424.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.120443 restraints weight = 11081.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.124115 restraints weight = 10382.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   7741  Z= 0.149
  Angle     :  0.602   9.291  10589  Z= 0.315
  Chirality :  0.049   0.183   1187
  Planarity :  0.004   0.047   1336
  Dihedral  : 10.441  78.169   1369
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.38 %
    Favored  : 88.62 %
  Rotamer:
    Outliers :  8.30 %
    Allowed  : 30.75 %
    Favored  : 60.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.28), residues: 975
  helix:  1.98 (0.39), residues: 207
  sheet: -0.84 (0.33), residues: 289
  loop : -2.95 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 259 
 HIS   0.004   0.001   HIS B 120 
 PHE   0.033   0.002   PHE C 152 
 TYR   0.017   0.001   TYR B  90 
 ARG   0.002   0.000   ARG C 175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02427 (  265)
  hydrogen bonds       : angle       4.40930 (  723)
  SS BOND              : bond        0.00352 (   15)
  SS BOND              : angle       1.07454 (   30)
  covalent geometry    : bond        0.00350 ( 7724)
  covalent geometry    : angle       0.60033 (10559)
  Misc. bond           : bond        0.00136 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2390.49 seconds
wall clock time: 42 minutes 41.28 seconds (2561.28 seconds total)