Starting phenix.real_space_refine
on Fri Feb 14 17:12:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d44_27174/02_2025/8d44_27174.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d44_27174/02_2025/8d44_27174.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d44_27174/02_2025/8d44_27174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d44_27174/02_2025/8d44_27174.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d44_27174/02_2025/8d44_27174.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d44_27174/02_2025/8d44_27174.cif"
  }
  resolution = 2.8
  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=  -0.000 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    6568      2.51       5
     N    1864      2.21       5
     O    1984      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10472
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "D"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329}
    Chain: "C"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329}
    Chain: "B"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329}
    Chain: "A"
      Number of atoms: 2618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2618
          Classifications: {'peptide': 343}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329}
  Time building chain proxies: 6.31, per 1000 atoms: 0.60
  Number of scatterers: 10472
  At special positions: 0
  Unit cell: (105.93, 82.39, 99.51, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1984      8.00
     N    1864      7.00
     C    6568      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.84
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2528

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      52.3% alpha, 13.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'D' and resid 9 through 24
      removed outlier: 3.783A  pdb=" N   VAL D  24 " --> pdb=" O   ALA D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 46
      removed outlier: 4.040A  pdb=" N   ARG D  46 " --> pdb=" O   ASN D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 64
    Processing helix  chain 'D' and resid 80 through 85
      removed outlier: 3.882A  pdb=" N   TYR D  85 " --> pdb=" O   HIS D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 101
    Processing helix  chain 'D' and resid 130 through 141
      removed outlier: 3.793A  pdb=" N   ARG D 134 " --> pdb=" O   GLY D 130 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 160 through 182
    Processing helix  chain 'D' and resid 198 through 220
    Processing helix  chain 'D' and resid 223 through 227
      removed outlier: 3.560A  pdb=" N   THR D 227 " --> pdb=" O   LEU D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 259
    Processing helix  chain 'D' and resid 276 through 289
    Processing helix  chain 'D' and resid 308 through 315
    Processing helix  chain 'D' and resid 320 through 338
      removed outlier: 3.686A  pdb=" N   ARG D 331 " --> pdb=" O   ALA D 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 3.786A  pdb=" N   VAL C  24 " --> pdb=" O   ALA C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 45
    Processing helix  chain 'C' and resid 46 through 48
      No H-bonds generated for 'chain 'C' and resid 46 through 48'
    Processing helix  chain 'C' and resid 52 through 65
    Processing helix  chain 'C' and resid 80 through 85
      removed outlier: 4.004A  pdb=" N   TYR C  85 " --> pdb=" O   HIS C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 101
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 160 through 182
    Processing helix  chain 'C' and resid 198 through 220
    Processing helix  chain 'C' and resid 223 through 227
      removed outlier: 3.719A  pdb=" N   THR C 227 " --> pdb=" O   LEU C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 261
      removed outlier: 3.547A  pdb=" N   ARG C 259 " --> pdb=" O   THR C 255 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 289
    Processing helix  chain 'C' and resid 308 through 315
    Processing helix  chain 'C' and resid 320 through 338
    Processing helix  chain 'B' and resid 9 through 24
      removed outlier: 3.794A  pdb=" N   VAL B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 45
    Processing helix  chain 'B' and resid 46 through 48
      No H-bonds generated for 'chain 'B' and resid 46 through 48'
    Processing helix  chain 'B' and resid 52 through 65
    Processing helix  chain 'B' and resid 67 through 72
      removed outlier: 3.712A  pdb=" N   ASN B  71 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 85
      removed outlier: 4.083A  pdb=" N   TYR B  85 " --> pdb=" O   HIS B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 101
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 160 through 181
    Processing helix  chain 'B' and resid 198 through 220
    Processing helix  chain 'B' and resid 223 through 227
      removed outlier: 3.723A  pdb=" N   THR B 227 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 259
      removed outlier: 3.625A  pdb=" N   ARG B 259 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 289
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 321 through 340
    Processing helix  chain 'A' and resid 9 through 24
      removed outlier: 3.771A  pdb=" N   VAL A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 45
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 52 through 65
    Processing helix  chain 'A' and resid 67 through 72
      removed outlier: 3.676A  pdb=" N   ASN A  71 " --> pdb=" O   SER A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 85
      removed outlier: 3.961A  pdb=" N   TYR A  85 " --> pdb=" O   HIS A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 101
    Processing helix  chain 'A' and resid 130 through 141
    Processing helix  chain 'A' and resid 160 through 182
    Processing helix  chain 'A' and resid 198 through 220
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 3.720A  pdb=" N   THR A 227 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 259
      removed outlier: 3.617A  pdb=" N   ARG A 259 " --> pdb=" O   THR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 289
    Processing helix  chain 'A' and resid 308 through 315
    Processing helix  chain 'A' and resid 321 through 338
    Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 32
      removed outlier: 6.970A  pdb=" N   GLY D  29 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   VAL D  77 " --> pdb=" O   GLY D  29 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   LEU D  31 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   LEU D  79 " --> pdb=" O   LEU D  31 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLY D  75 " --> pdb=" O   VAL D 104 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   GLY D 106 " --> pdb=" O   GLY D  75 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL D  77 " --> pdb=" O   GLY D 106 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   LYS D 108 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   LEU D  79 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL D 105 " --> pdb=" O   PHE D 145 " (cutoff:3.500A)
      removed outlier: 8.343A  pdb=" N   LYS D 147 " --> pdb=" O   VAL D 105 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ILE D 107 " --> pdb=" O   LYS D 147 " (cutoff:3.500A)
      removed outlier: 8.552A  pdb=" N   ARG D 149 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 5.804A  pdb=" N   LEU D 229 " --> pdb=" O   CYS D 269 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ILE D 268 " --> pdb=" O   SER D 299 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   SER D 301 " --> pdb=" O   ILE D 268 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   PHE D 270 " --> pdb=" O   SER D 301 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 112 through 115
    Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 32
      removed outlier: 7.067A  pdb=" N   GLY C  29 " --> pdb=" O   GLY C  75 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   VAL C  77 " --> pdb=" O   GLY C  29 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   LEU C  31 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   LEU C  79 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   GLY C  75 " --> pdb=" O   VAL C 104 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   GLY C 106 " --> pdb=" O   GLY C  75 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   VAL C  77 " --> pdb=" O   GLY C 106 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   LYS C 108 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   LEU C  79 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL C 105 " --> pdb=" O   PHE C 145 " (cutoff:3.500A)
      removed outlier: 8.294A  pdb=" N   LYS C 147 " --> pdb=" O   VAL C 105 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ILE C 107 " --> pdb=" O   LYS C 147 " (cutoff:3.500A)
      removed outlier: 8.515A  pdb=" N   ARG C 149 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   LEU C 229 " --> pdb=" O   CYS C 269 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ILE C 268 " --> pdb=" O   SER C 299 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   SER C 301 " --> pdb=" O   ILE C 268 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   PHE C 270 " --> pdb=" O   SER C 301 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 112 through 115
    Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 32
      removed outlier: 7.088A  pdb=" N   GLY B  29 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL B  77 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   LEU B  31 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   VAL B 105 " --> pdb=" O   PHE B 145 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   LYS B 147 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE B 107 " --> pdb=" O   LYS B 147 " (cutoff:3.500A)
      removed outlier: 8.538A  pdb=" N   ARG B 149 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   LEU B 229 " --> pdb=" O   CYS B 269 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ILE B 268 " --> pdb=" O   SER B 299 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   SER B 301 " --> pdb=" O   ILE B 268 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   PHE B 270 " --> pdb=" O   SER B 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 115
    Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32
      removed outlier: 7.059A  pdb=" N   GLY A  29 " --> pdb=" O   GLY A  75 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   VAL A  77 " --> pdb=" O   GLY A  29 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   LEU A  31 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   LEU A  79 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL A 105 " --> pdb=" O   PHE A 145 " (cutoff:3.500A)
      removed outlier: 8.329A  pdb=" N   LYS A 147 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE A 107 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 8.529A  pdb=" N   ARG A 149 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   LEU A 229 " --> pdb=" O   CYS A 269 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   ILE A 268 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   SER A 301 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   PHE A 270 " --> pdb=" O   SER A 301 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 115

    551 hydrogen bonds defined for protein.
    1611 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: 3.29

  Time building geometry restraints manager: 3.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2220
        1.33 -     1.45: 2245
        1.45 -     1.57: 6103
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 10648
  Sorted by residual:
  bond pdb=" C   MET B 251 "
       pdb=" O   MET B 251 "
    ideal  model  delta    sigma   weight residual
    1.236  1.206  0.031 1.15e-02 7.56e+03 7.20e+00
  bond pdb=" CA  ALA B 250 "
       pdb=" C   ALA B 250 "
    ideal  model  delta    sigma   weight residual
    1.524  1.495  0.029 1.27e-02 6.20e+03 5.05e+00
  bond pdb=" CA  MET B 251 "
       pdb=" C   MET B 251 "
    ideal  model  delta    sigma   weight residual
    1.524  1.497  0.026 1.27e-02 6.20e+03 4.33e+00
  bond pdb=" C   THR B 253 "
       pdb=" O   THR B 253 "
    ideal  model  delta    sigma   weight residual
    1.236  1.216  0.021 1.15e-02 7.56e+03 3.33e+00
  bond pdb=" CA  ALA B 250 "
       pdb=" CB  ALA B 250 "
    ideal  model  delta    sigma   weight residual
    1.529  1.506  0.023 1.55e-02 4.16e+03 2.25e+00
  ... (remaining 10643 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 14174
        2.13 -     4.25: 197
        4.25 -     6.38: 22
        6.38 -     8.51: 2
        8.51 -    10.63: 1
  Bond angle restraints: 14396
  Sorted by residual:
  angle pdb=" CB  MET A 251 "
        pdb=" CG  MET A 251 "
        pdb=" SD  MET A 251 "
      ideal   model   delta    sigma   weight residual
     112.70  123.33  -10.63 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" CA  GLN C  90 "
        pdb=" CB  GLN C  90 "
        pdb=" CG  GLN C  90 "
      ideal   model   delta    sigma   weight residual
     114.10  120.93   -6.83 2.00e+00 2.50e-01 1.17e+01
  angle pdb=" CB  GLN B  58 "
        pdb=" CG  GLN B  58 "
        pdb=" CD  GLN B  58 "
      ideal   model   delta    sigma   weight residual
     112.60  117.75   -5.15 1.70e+00 3.46e-01 9.19e+00
  angle pdb=" CB  GLU D 322 "
        pdb=" CG  GLU D 322 "
        pdb=" CD  GLU D 322 "
      ideal   model   delta    sigma   weight residual
     112.60  117.59   -4.99 1.70e+00 3.46e-01 8.62e+00
  angle pdb=" CB  GLU D 326 "
        pdb=" CG  GLU D 326 "
        pdb=" CD  GLU D 326 "
      ideal   model   delta    sigma   weight residual
     112.60  117.53   -4.93 1.70e+00 3.46e-01 8.40e+00
  ... (remaining 14391 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 5621
       17.79 -    35.59: 623
       35.59 -    53.38: 196
       53.38 -    71.17: 33
       71.17 -    88.97: 15
  Dihedral angle restraints: 6488
    sinusoidal: 2556
      harmonic: 3932
  Sorted by residual:
  dihedral pdb=" CA  ALA C 338 "
           pdb=" C   ALA C 338 "
           pdb=" N   ALA C 339 "
           pdb=" CA  ALA C 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.37   17.63     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  GLN A 111 "
           pdb=" C   GLN A 111 "
           pdb=" N   GLY A 112 "
           pdb=" CA  GLY A 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.26   16.74     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  VAL C  24 "
           pdb=" C   VAL C  24 "
           pdb=" N   ALA C  25 "
           pdb=" CA  ALA C  25 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.58  -16.42     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 6485 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 940
       0.027 -    0.055: 387
       0.055 -    0.082: 158
       0.082 -    0.110: 106
       0.110 -    0.137: 33
  Chirality restraints: 1624
  Sorted by residual:
  chirality pdb=" CA  TYR D 214 "
            pdb=" N   TYR D 214 "
            pdb=" C   TYR D 214 "
            pdb=" CB  TYR D 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  VAL C 187 "
            pdb=" N   VAL C 187 "
            pdb=" C   VAL C 187 "
            pdb=" CB  VAL C 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  VAL A 187 "
            pdb=" N   VAL A 187 "
            pdb=" C   VAL A 187 "
            pdb=" CB  VAL A 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 1621 not shown)

  Planarity restraints: 1888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 114 "   -0.047 5.00e-02 4.00e+02   7.14e-02 8.15e+00
        pdb=" N   PRO B 115 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 115 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 115 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 114 "   -0.045 5.00e-02 4.00e+02   6.84e-02 7.49e+00
        pdb=" N   PRO C 115 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO C 115 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C 115 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 114 "    0.042 5.00e-02 4.00e+02   6.47e-02 6.69e+00
        pdb=" N   PRO A 115 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO A 115 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 115 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1885 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1770
        2.77 -     3.30: 9787
        3.30 -     3.83: 18980
        3.83 -     4.37: 22189
        4.37 -     4.90: 37800
  Nonbonded interactions: 90526
  Sorted by model distance:
  nonbonded pdb=" O   GLU D  61 "
            pdb=" OG  SER D  65 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   LEU A 116 "
            pdb=" OG1 THR A 119 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   LEU B 116 "
            pdb=" OG1 THR B 119 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" NH1 ARG B 149 "
            pdb=" OE1 GLU B 190 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   LEU D 116 "
            pdb=" OG1 THR D 119 "
     model   vdw
     2.272 3.040
  ... (remaining 90521 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.270
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  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:11.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
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   0.039  10648  Z= 0.251
  Angle     :  0.628  10.635  14396  Z= 0.353
  Chirality :  0.043   0.137   1624
  Planarity :  0.006   0.071   1888
  Dihedral  : 16.987  88.965   3960
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.82 %
    Favored  : 82.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.23), residues: 1364
  helix:  1.65 (0.19), residues: 668
  sheet: -1.68 (0.29), residues: 248
  loop : -0.60 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 148 
 HIS   0.006   0.001   HIS C 197 
 PHE   0.012   0.002   PHE C 145 
 TYR   0.019   0.002   TYR B 174 
 ARG   0.003   0.000   ARG B  57 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.076 
Fit side-chains
REVERT: D  110 ASP cc_start: 0.8200 (p0) cc_final: 0.7981 (p0)
REVERT: C  296 TRP cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (m-90)
REVERT: B  110 ASP cc_start: 0.8277 (p0) cc_final: 0.7942 (p0)
REVERT: A  110 ASP cc_start: 0.8345 (p0) cc_final: 0.8119 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 138
  average time/residue: 1.2071
  time to fit residues: 180.1782
Evaluate side-chains
  129 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   82 GLU
Chi-restraints excluded: chain D residue  129 ASP
Chi-restraints excluded: chain D residue  292 LEU
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  129 ASP
Chi-restraints excluded: chain C residue  164 ILE
Chi-restraints excluded: chain C residue  202 CYS
Chi-restraints excluded: chain C residue  251 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue  129 ASP
Chi-restraints excluded: chain A residue  202 CYS
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 106 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0970
   chunk 79 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  90 GLN
C 258 HIS
C 335 ASN
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.182704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.141816 restraints weight = 9867.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.52
r_work: 0.3493 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.0781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10648  Z= 0.285
  Angle     :  0.564   5.254  14396  Z= 0.302
  Chirality :  0.043   0.137   1624
  Planarity :  0.005   0.052   1888
  Dihedral  :  5.542  47.661   1486
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.09 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.23), residues: 1364
  helix:  1.94 (0.19), residues: 672
  sheet: -1.75 (0.29), residues: 248
  loop : -0.47 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 148 
 HIS   0.005   0.001   HIS C 197 
 PHE   0.013   0.002   PHE A 145 
 TYR   0.017   0.002   TYR C 214 
 ARG   0.005   0.000   ARG B 149 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.199 
Fit side-chains
REVERT: D  110 ASP cc_start: 0.8136 (p0) cc_final: 0.7889 (p0)
REVERT: C  110 ASP cc_start: 0.8317 (p0) cc_final: 0.8098 (p0)
REVERT: C  174 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7841 (t80)
REVERT: C  251 MET cc_start: 0.7710 (tpp) cc_final: 0.7321 (tpp)
REVERT: B  110 ASP cc_start: 0.8307 (p0) cc_final: 0.8073 (p0)
REVERT: B  174 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7927 (t80)
REVERT: A  110 ASP cc_start: 0.8130 (p0) cc_final: 0.7867 (p0)
REVERT: A  174 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7836 (t80)
  outliers start: 22
  outliers final: 7
  residues processed: 145
  average time/residue: 1.1880
  time to fit residues: 186.5353
Evaluate side-chains
  127 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  164 ILE
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  275 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 126 optimal weight:    0.8980
   chunk 105 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   chunk 96 optimal weight:    0.6980
   chunk 122 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 70 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0670
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
D  90 GLN
D 258 HIS
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.176765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130378 restraints weight = 10086.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.88
r_work: 0.3422 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10648  Z= 0.203
  Angle     :  0.500   5.385  14396  Z= 0.269
  Chirality :  0.040   0.130   1624
  Planarity :  0.005   0.048   1888
  Dihedral  :  4.916  45.274   1470
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.00 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.03 (0.23), residues: 1364
  helix:  2.23 (0.19), residues: 672
  sheet: -1.54 (0.30), residues: 228
  loop : -0.38 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 148 
 HIS   0.004   0.001   HIS C 197 
 PHE   0.013   0.001   PHE B 145 
 TYR   0.012   0.001   TYR C 214 
 ARG   0.003   0.000   ARG D  57 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 1.143 
Fit side-chains
REVERT: D  174 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7762 (t80)
REVERT: C   80 PHE cc_start: 0.7059 (t80) cc_final: 0.6843 (t80)
REVERT: C  174 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7777 (t80)
REVERT: C  248 GLN cc_start: 0.7933 (mt0) cc_final: 0.7659 (mt0)
REVERT: C  251 MET cc_start: 0.7532 (tpp) cc_final: 0.7013 (tpp)
REVERT: B  110 ASP cc_start: 0.8173 (p0) cc_final: 0.7903 (p0)
REVERT: B  174 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7827 (t80)
REVERT: A  110 ASP cc_start: 0.7899 (p0) cc_final: 0.7675 (p0)
REVERT: A  174 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7699 (t80)
  outliers start: 22
  outliers final: 8
  residues processed: 153
  average time/residue: 1.2987
  time to fit residues: 213.9889
Evaluate side-chains
  130 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  126 GLN
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  275 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 106 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0060
   chunk 125 optimal weight:    0.2980
   chunk 131 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 109 optimal weight:    0.5980
   chunk 89 optimal weight:    0.5980
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
C  90 GLN
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.178330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.134219 restraints weight = 9941.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.98
r_work: 0.3437 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10648  Z= 0.175
  Angle     :  0.475   5.455  14396  Z= 0.255
  Chirality :  0.040   0.126   1624
  Planarity :  0.004   0.048   1888
  Dihedral  :  4.727  46.089   1468
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 17.09 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.23), residues: 1364
  helix:  2.48 (0.19), residues: 672
  sheet: -1.49 (0.30), residues: 228
  loop : -0.32 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 148 
 HIS   0.007   0.001   HIS D 258 
 PHE   0.012   0.001   PHE D  59 
 TYR   0.011   0.001   TYR D 214 
 ARG   0.003   0.000   ARG D  57 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 1.174 
Fit side-chains
REVERT: C   80 PHE cc_start: 0.7088 (t80) cc_final: 0.6886 (t80)
REVERT: C  248 GLN cc_start: 0.7914 (mt0) cc_final: 0.7611 (mt0)
REVERT: C  251 MET cc_start: 0.7486 (tpp) cc_final: 0.6974 (tpp)
REVERT: B  110 ASP cc_start: 0.8078 (p0) cc_final: 0.7829 (p0)
REVERT: B  174 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7770 (t80)
REVERT: B  251 MET cc_start: 0.7078 (tpp) cc_final: 0.6629 (tpp)
REVERT: A  110 ASP cc_start: 0.7857 (p0) cc_final: 0.7640 (p0)
REVERT: A  149 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8156 (ttt90)
REVERT: A  251 MET cc_start: 0.7561 (tpp) cc_final: 0.7353 (tpp)
  outliers start: 21
  outliers final: 5
  residues processed: 151
  average time/residue: 1.2343
  time to fit residues: 201.3301
Evaluate side-chains
  121 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 134 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0870
   chunk 5 optimal weight:    5.9990
   chunk 115 optimal weight:    0.1980
   chunk 114 optimal weight:    0.0270
   chunk 22 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.3416

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

Flipped N/Q/H residues before XYZ refinement:
C  90 GLN
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.179167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.135980 restraints weight = 10028.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.85
r_work: 0.3448 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10648  Z= 0.160
  Angle     :  0.461   5.445  14396  Z= 0.247
  Chirality :  0.039   0.124   1624
  Planarity :  0.004   0.048   1888
  Dihedral  :  4.613  46.545   1468
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 17.27 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.44 (0.23), residues: 1364
  helix:  2.67 (0.19), residues: 672
  sheet: -1.46 (0.30), residues: 228
  loop : -0.28 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 148 
 HIS   0.005   0.001   HIS D 258 
 PHE   0.012   0.001   PHE D  59 
 TYR   0.012   0.001   TYR A 204 
 ARG   0.003   0.000   ARG D  57 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 1.129 
Fit side-chains
REVERT: C  100 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6679 (mp0)
REVERT: C  110 ASP cc_start: 0.8013 (p0) cc_final: 0.7758 (p0)
REVERT: C  248 GLN cc_start: 0.7942 (mt0) cc_final: 0.7635 (mt0)
REVERT: C  251 MET cc_start: 0.7553 (tpp) cc_final: 0.7070 (tpp)
REVERT: B  110 ASP cc_start: 0.8073 (p0) cc_final: 0.7794 (p0)
REVERT: B  174 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7823 (t80)
REVERT: B  251 MET cc_start: 0.7109 (tpp) cc_final: 0.6724 (tpp)
REVERT: A  251 MET cc_start: 0.7706 (tpp) cc_final: 0.7359 (tpp)
  outliers start: 21
  outliers final: 7
  residues processed: 146
  average time/residue: 1.1667
  time to fit residues: 184.8023
Evaluate side-chains
  124 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  275 MET
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue   97 ILE
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 89 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 47 optimal weight:    0.4980
   chunk 125 optimal weight:    1.9990
   chunk 132 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
D  90 GLN
C 258 HIS
B  86 GLN
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.175474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.132061 restraints weight = 10052.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.95
r_work: 0.3409 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  10648  Z= 0.249
  Angle     :  0.522   5.086  14396  Z= 0.279
  Chirality :  0.042   0.134   1624
  Planarity :  0.004   0.047   1888
  Dihedral  :  4.866  48.001   1468
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.82 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.23), residues: 1364
  helix:  2.53 (0.19), residues: 672
  sheet: -1.38 (0.30), residues: 224
  loop : -0.41 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 148 
 HIS   0.008   0.001   HIS D 258 
 PHE   0.013   0.002   PHE A  59 
 TYR   0.017   0.002   TYR D 214 
 ARG   0.003   0.000   ARG A 153 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.135 
Fit side-chains
REVERT: D   42 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7688 (t0)
REVERT: D  174 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: C  174 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7771 (t80)
REVERT: C  251 MET cc_start: 0.7533 (tpp) cc_final: 0.6963 (tpp)
REVERT: B  110 ASP cc_start: 0.8147 (p0) cc_final: 0.7890 (p0)
REVERT: B  174 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7866 (t80)
REVERT: B  251 MET cc_start: 0.7054 (tpp) cc_final: 0.6581 (tpp)
REVERT: A  110 ASP cc_start: 0.7854 (p0) cc_final: 0.7553 (p0)
REVERT: A  174 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7841 (t80)
REVERT: A  251 MET cc_start: 0.7700 (tpp) cc_final: 0.7429 (tpp)
  outliers start: 22
  outliers final: 6
  residues processed: 144
  average time/residue: 1.1837
  time to fit residues: 184.4013
Evaluate side-chains
  129 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   42 ASN
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 109 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 130 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
D 258 HIS
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.174935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.128843 restraints weight = 10142.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 2.09
r_work: 0.3372 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030  10648  Z= 0.307
  Angle     :  0.558   5.176  14396  Z= 0.299
  Chirality :  0.043   0.140   1624
  Planarity :  0.005   0.046   1888
  Dihedral  :  5.084  50.382   1468
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.64 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.09 (0.23), residues: 1364
  helix:  2.33 (0.19), residues: 676
  sheet: -1.46 (0.31), residues: 224
  loop : -0.51 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 148 
 HIS   0.005   0.001   HIS D 258 
 PHE   0.014   0.002   PHE B 145 
 TYR   0.016   0.002   TYR D 214 
 ARG   0.003   0.000   ARG A 153 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.209 
Fit side-chains
REVERT: D  174 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7767 (t80)
REVERT: C  110 ASP cc_start: 0.8184 (p0) cc_final: 0.7962 (p0)
REVERT: C  174 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7771 (t80)
REVERT: C  251 MET cc_start: 0.7580 (tpp) cc_final: 0.7114 (tpp)
REVERT: B  174 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7879 (t80)
REVERT: B  251 MET cc_start: 0.7195 (tpp) cc_final: 0.6711 (tpp)
REVERT: A  110 ASP cc_start: 0.7953 (p0) cc_final: 0.7720 (p0)
REVERT: A  174 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7834 (t80)
REVERT: A  200 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7644 (mp0)
REVERT: A  251 MET cc_start: 0.7788 (tpp) cc_final: 0.7500 (tpp)
  outliers start: 23
  outliers final: 7
  residues processed: 142
  average time/residue: 1.2079
  time to fit residues: 185.9118
Evaluate side-chains
  133 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 119 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
D  90 GLN
D 258 HIS
C  90 GLN
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.173746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.127636 restraints weight = 10066.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.22
r_work: 0.3367 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  10648  Z= 0.316
  Angle     :  0.568   5.226  14396  Z= 0.303
  Chirality :  0.043   0.141   1624
  Planarity :  0.005   0.046   1888
  Dihedral  :  5.174  50.801   1468
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.18 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.23), residues: 1364
  helix:  2.24 (0.19), residues: 676
  sheet: -1.67 (0.29), residues: 244
  loop : -0.51 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 148 
 HIS   0.004   0.001   HIS C 197 
 PHE   0.015   0.002   PHE B 145 
 TYR   0.015   0.002   TYR D 214 
 ARG   0.003   0.000   ARG A 153 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 1.265 
Fit side-chains
REVERT: D   90 GLN cc_start: 0.6684 (OUTLIER) cc_final: 0.6471 (mt0)
REVERT: D  110 ASP cc_start: 0.8308 (p0) cc_final: 0.7993 (p0)
REVERT: D  174 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.7769 (t80)
REVERT: C  110 ASP cc_start: 0.8193 (p0) cc_final: 0.7970 (p0)
REVERT: C  174 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7807 (t80)
REVERT: C  251 MET cc_start: 0.7608 (tpp) cc_final: 0.7115 (tpp)
REVERT: B  174 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7886 (t80)
REVERT: B  251 MET cc_start: 0.7206 (tpp) cc_final: 0.6702 (tpp)
REVERT: A  174 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7834 (t80)
REVERT: A  200 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7630 (mp0)
REVERT: A  251 MET cc_start: 0.7768 (tpp) cc_final: 0.7467 (tpp)
  outliers start: 24
  outliers final: 7
  residues processed: 141
  average time/residue: 1.2384
  time to fit residues: 188.7273
Evaluate side-chains
  135 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 GLN
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  200 GLU
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 94 optimal weight:    0.3980
   chunk 81 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 132 optimal weight:    0.8980
   chunk 123 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
D  90 GLN
D 258 HIS
C  90 GLN
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.175366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.131088 restraints weight = 10114.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.11
r_work: 0.3408 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10648  Z= 0.222
  Angle     :  0.515   5.125  14396  Z= 0.277
  Chirality :  0.041   0.131   1624
  Planarity :  0.004   0.046   1888
  Dihedral  :  5.023  51.101   1468
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.00 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.13 (0.23), residues: 1364
  helix:  2.44 (0.19), residues: 672
  sheet: -1.67 (0.29), residues: 244
  loop : -0.37 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 148 
 HIS   0.003   0.001   HIS C 197 
 PHE   0.014   0.002   PHE B 145 
 TYR   0.011   0.002   TYR A 214 
 ARG   0.004   0.000   ARG D  57 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.121 
Fit side-chains
REVERT: D  100 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6820 (mp0)
REVERT: D  110 ASP cc_start: 0.8167 (p0) cc_final: 0.7829 (p0)
REVERT: D  174 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7753 (t80)
REVERT: C  174 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7766 (t80)
REVERT: C  251 MET cc_start: 0.7563 (tpp) cc_final: 0.7100 (tpp)
REVERT: B  174 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7862 (t80)
REVERT: B  251 MET cc_start: 0.7221 (tpp) cc_final: 0.6737 (tpp)
REVERT: A  110 ASP cc_start: 0.7865 (p0) cc_final: 0.7553 (p0)
REVERT: A  174 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7780 (t80)
REVERT: A  251 MET cc_start: 0.7786 (tpp) cc_final: 0.7482 (tpp)
  outliers start: 17
  outliers final: 7
  residues processed: 141
  average time/residue: 1.1950
  time to fit residues: 183.0263
Evaluate side-chains
  131 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 93 optimal weight:    0.6980
   chunk 106 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 105 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
D  90 GLN
D 258 HIS
C  90 GLN
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.171631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.127963 restraints weight = 10098.606|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.71
r_work: 0.3308 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  10648  Z= 0.434
  Angle     :  0.642   6.163  14396  Z= 0.341
  Chirality :  0.047   0.152   1624
  Planarity :  0.005   0.047   1888
  Dihedral  :  5.395  51.148   1468
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 18.45 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.23), residues: 1364
  helix:  2.05 (0.19), residues: 676
  sheet: -1.76 (0.29), residues: 244
  loop : -0.55 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP C 148 
 HIS   0.004   0.001   HIS C 197 
 PHE   0.016   0.002   PHE B 145 
 TYR   0.016   0.002   TYR B 214 
 ARG   0.005   0.001   ARG A 149 

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

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

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2728 Ramachandran restraints generated.
    1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 1.191 
Fit side-chains
REVERT: D  174 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.7806 (t80)
REVERT: C  174 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7893 (t80)
REVERT: C  251 MET cc_start: 0.7777 (tpp) cc_final: 0.7273 (tpp)
REVERT: B  174 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.7890 (t80)
REVERT: B  251 MET cc_start: 0.7459 (tpp) cc_final: 0.7090 (tpp)
REVERT: A  174 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7856 (t80)
REVERT: A  251 MET cc_start: 0.7902 (tpp) cc_final: 0.7588 (tpp)
  outliers start: 22
  outliers final: 8
  residues processed: 127
  average time/residue: 1.2772
  time to fit residues: 175.3495
Evaluate side-chains
  124 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  129 ASP
Chi-restraints excluded: chain D residue  174 TYR
Chi-restraints excluded: chain D residue  296 TRP
Chi-restraints excluded: chain C residue  174 TYR
Chi-restraints excluded: chain C residue  296 TRP
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  296 TRP
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  174 TYR
Chi-restraints excluded: chain A residue  296 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 23 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 135 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D 258 HIS
C  90 GLN
C 221 HIS
C 258 HIS
B 258 HIS
A 258 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.175300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.128784 restraints weight = 10007.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.86
r_work: 0.3372 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10648  Z= 0.214
  Angle     :  0.515   5.285  14396  Z= 0.278
  Chirality :  0.041   0.132   1624
  Planarity :  0.004   0.046   1888
  Dihedral  :  5.037  51.468   1468
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.18 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  1.06 (0.23), residues: 1364
  helix:  2.40 (0.19), residues: 672
  sheet: -1.73 (0.29), residues: 244
  loop : -0.41 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 148 
 HIS   0.004   0.001   HIS C 197 
 PHE   0.013   0.002   PHE A 145 
 TYR   0.012   0.001   TYR A 214 
 ARG   0.004   0.000   ARG D  57 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7350.49 seconds
wall clock time: 130 minutes 38.35 seconds (7838.35 seconds total)