Starting phenix.real_space_refine
on Sat Aug 23 03:49:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yu7_39573/08_2025/8yu7_39573.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yu7_39573/08_2025/8yu7_39573.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yu7_39573/08_2025/8yu7_39573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yu7_39573/08_2025/8yu7_39573.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yu7_39573/08_2025/8yu7_39573.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yu7_39573/08_2025/8yu7_39573.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.103
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      48      5.16       5
     C    6612      2.51       5
     N    1436      2.21       5
     O    1520      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9616
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2264
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
    Chain: "B"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2264
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
    Chain: "C"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2264
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
    Chain: "D"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2264
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 269}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 9
    Chain: "A"
      Number of atoms: 168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 168
          Unusual residues: {'CLR': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 140
          Unusual residues: {'CLR': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "C"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 112
          Unusual residues: {'CLR': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "D"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 140
          Unusual residues: {'CLR': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 1.80, per 1000 atoms: 0.19
  Number of scatterers: 9616
  At special positions: 0
  Unit cell: (94.35, 94.35, 79.9, 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      48     16.00
     O    1520      8.00
     N    1436      7.00
     C    6612      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 109 " - pdb=" SG  CYS A 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  28 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 109 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  28 " - pdb=" SG  CYS C 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 109 " - pdb=" SG  CYS C 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  28 " - pdb=" SG  CYS D 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 109 " - pdb=" SG  CYS D 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  Conformation dependent library (CDL) restraints added in 355.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      81.4% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 64
      Proline residue:  A  42  - end of helix
    Processing helix  chain 'A' and resid 72 through 100
      removed outlier: 4.173A  pdb=" N   TYR A  76 " --> pdb=" O   MET A  72 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
      removed outlier: 3.790A  pdb=" N   VAL A  99 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 140
      removed outlier: 3.574A  pdb=" N   LYS A 110 " --> pdb=" O   ASN A 106 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   LEU A 125 " --> pdb=" O   TYR A 121 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   HIS A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 175
      Proline residue:  A 163  - end of helix
      Proline residue:  A 170  - end of helix
      removed outlier: 3.694A  pdb=" N   ILE A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 208
      removed outlier: 3.805A  pdb=" N   VAL A 196 " --> pdb=" O   ASN A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 226
      removed outlier: 3.742A  pdb=" N   VAL A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
    Processing helix  chain 'A' and resid 238 through 251
    Processing helix  chain 'A' and resid 252 through 267
    Processing helix  chain 'A' and resid 274 through 305
      removed outlier: 4.147A  pdb=" N   ASN A 278 " --> pdb=" O   CYS A 274 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   THR A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      Proline residue:  A 299  - end of helix
      removed outlier: 3.959A  pdb=" N   LEU A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 36 through 64
      Proline residue:  B  42  - end of helix
    Processing helix  chain 'B' and resid 72 through 100
      removed outlier: 4.173A  pdb=" N   TYR B  76 " --> pdb=" O   MET B  72 " (cutoff:3.500A)
      Proline residue:  B  92  - end of helix
      removed outlier: 3.790A  pdb=" N   VAL B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 140
      removed outlier: 3.574A  pdb=" N   LYS B 110 " --> pdb=" O   ASN B 106 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LEU B 125 " --> pdb=" O   TYR B 121 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   HIS B 140 " --> pdb=" O   LEU B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 175
      Proline residue:  B 163  - end of helix
      Proline residue:  B 170  - end of helix
      removed outlier: 3.693A  pdb=" N   ILE B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 208
      removed outlier: 3.805A  pdb=" N   VAL B 196 " --> pdb=" O   ASN B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 226
      removed outlier: 3.742A  pdb=" N   VAL B 214 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 238 through 251
    Processing helix  chain 'B' and resid 252 through 267
    Processing helix  chain 'B' and resid 274 through 305
      removed outlier: 4.148A  pdb=" N   ASN B 278 " --> pdb=" O   CYS B 274 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   THR B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      Proline residue:  B 299  - end of helix
      removed outlier: 3.960A  pdb=" N   LEU B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 64
      Proline residue:  C  42  - end of helix
    Processing helix  chain 'C' and resid 72 through 100
      removed outlier: 4.173A  pdb=" N   TYR C  76 " --> pdb=" O   MET C  72 " (cutoff:3.500A)
      Proline residue:  C  92  - end of helix
      removed outlier: 3.789A  pdb=" N   VAL C  99 " --> pdb=" O   ALA C  95 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ALA C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 140
      removed outlier: 3.573A  pdb=" N   LYS C 110 " --> pdb=" O   ASN C 106 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL C 124 " --> pdb=" O   LEU C 120 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LEU C 125 " --> pdb=" O   TYR C 121 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   HIS C 140 " --> pdb=" O   LEU C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 175
      Proline residue:  C 163  - end of helix
      Proline residue:  C 170  - end of helix
      removed outlier: 3.694A  pdb=" N   ILE C 173 " --> pdb=" O   ILE C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 208
      removed outlier: 3.804A  pdb=" N   VAL C 196 " --> pdb=" O   ASN C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 226
      removed outlier: 3.742A  pdb=" N   VAL C 214 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 237
    Processing helix  chain 'C' and resid 238 through 251
    Processing helix  chain 'C' and resid 252 through 267
    Processing helix  chain 'C' and resid 274 through 305
      removed outlier: 4.147A  pdb=" N   ASN C 278 " --> pdb=" O   CYS C 274 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   THR C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
      Proline residue:  C 299  - end of helix
      removed outlier: 3.959A  pdb=" N   LEU C 305 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 36 through 64
      Proline residue:  D  42  - end of helix
    Processing helix  chain 'D' and resid 72 through 100
      removed outlier: 4.173A  pdb=" N   TYR D  76 " --> pdb=" O   MET D  72 " (cutoff:3.500A)
      Proline residue:  D  92  - end of helix
      removed outlier: 3.789A  pdb=" N   VAL D  99 " --> pdb=" O   ALA D  95 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ALA D 100 " --> pdb=" O   VAL D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 140
      removed outlier: 3.573A  pdb=" N   LYS D 110 " --> pdb=" O   ASN D 106 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL D 124 " --> pdb=" O   LEU D 120 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LEU D 125 " --> pdb=" O   TYR D 121 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   HIS D 140 " --> pdb=" O   LEU D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 145 through 175
      Proline residue:  D 163  - end of helix
      Proline residue:  D 170  - end of helix
      removed outlier: 3.693A  pdb=" N   ILE D 173 " --> pdb=" O   ILE D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 192 through 208
      removed outlier: 3.805A  pdb=" N   VAL D 196 " --> pdb=" O   ASN D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 226
      removed outlier: 3.742A  pdb=" N   VAL D 214 " --> pdb=" O   LEU D 210 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 232 through 237
    Processing helix  chain 'D' and resid 238 through 251
    Processing helix  chain 'D' and resid 252 through 267
    Processing helix  chain 'D' and resid 274 through 305
      removed outlier: 4.146A  pdb=" N   ASN D 278 " --> pdb=" O   CYS D 274 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   THR D 279 " --> pdb=" O   GLU D 275 " (cutoff:3.500A)
      Proline residue:  D 299  - end of helix
      removed outlier: 3.959A  pdb=" N   LEU D 305 " --> pdb=" O   LEU D 301 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178
      removed outlier: 3.595A  pdb=" N   ILE A 185 " --> pdb=" O   SER A 178 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 177 through 178
      removed outlier: 3.595A  pdb=" N   ILE B 185 " --> pdb=" O   SER B 178 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 178
      removed outlier: 3.595A  pdb=" N   ILE C 185 " --> pdb=" O   SER C 178 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 177 through 178
      removed outlier: 3.595A  pdb=" N   ILE D 185 " --> pdb=" O   SER D 178 " (cutoff:3.500A)

    644 hydrogen bonds defined for protein.
    1932 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: 1.53

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2675
        1.34 -     1.46: 2045
        1.46 -     1.58: 5152
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 9932
  Sorted by residual:
  bond pdb=" C13 CLR B 403 "
       pdb=" C17 CLR B 403 "
    ideal  model  delta    sigma   weight residual
    1.550  1.484  0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" C13 CLR A 406 "
       pdb=" C17 CLR A 406 "
    ideal  model  delta    sigma   weight residual
    1.550  1.485  0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" C13 CLR A 402 "
       pdb=" C17 CLR A 402 "
    ideal  model  delta    sigma   weight residual
    1.550  1.485  0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" C13 CLR D 401 "
       pdb=" C17 CLR D 401 "
    ideal  model  delta    sigma   weight residual
    1.550  1.489  0.061 2.00e-02 2.50e+03 9.24e+00
  bond pdb=" C13 CLR A 405 "
       pdb=" C17 CLR A 405 "
    ideal  model  delta    sigma   weight residual
    1.550  1.489  0.061 2.00e-02 2.50e+03 9.24e+00
  ... (remaining 9927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.84: 13230
        2.84 -     5.68: 332
        5.68 -     8.51: 76
        8.51 -    11.35: 17
       11.35 -    14.19: 5
  Bond angle restraints: 13660
  Sorted by residual:
  angle pdb=" C13 CLR D 402 "
        pdb=" C14 CLR D 402 "
        pdb=" C8  CLR D 402 "
      ideal   model   delta    sigma   weight residual
     115.50  101.31   14.19 3.00e+00 1.11e-01 2.24e+01
  angle pdb=" N   GLY B 159 "
        pdb=" CA  GLY B 159 "
        pdb=" C   GLY B 159 "
      ideal   model   delta    sigma   weight residual
     113.27  118.88   -5.61 1.33e+00 5.65e-01 1.78e+01
  angle pdb=" N   GLY D 159 "
        pdb=" CA  GLY D 159 "
        pdb=" C   GLY D 159 "
      ideal   model   delta    sigma   weight residual
     113.27  118.88   -5.61 1.33e+00 5.65e-01 1.78e+01
  angle pdb=" N   GLY A 159 "
        pdb=" CA  GLY A 159 "
        pdb=" C   GLY A 159 "
      ideal   model   delta    sigma   weight residual
     113.27  118.88   -5.61 1.33e+00 5.65e-01 1.78e+01
  angle pdb=" N   GLY C 159 "
        pdb=" CA  GLY C 159 "
        pdb=" C   GLY C 159 "
      ideal   model   delta    sigma   weight residual
     113.27  118.85   -5.58 1.33e+00 5.65e-01 1.76e+01
  ... (remaining 13655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 5540
       17.05 -    34.10: 924
       34.10 -    51.14: 177
       51.14 -    68.19: 47
       68.19 -    85.24: 20
  Dihedral angle restraints: 6708
    sinusoidal: 3384
      harmonic: 3324
  Sorted by residual:
  dihedral pdb=" CA  ILE A 173 "
           pdb=" C   ILE A 173 "
           pdb=" N   PHE A 174 "
           pdb=" CA  PHE A 174 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.15  -16.85     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CA  ILE C 173 "
           pdb=" C   ILE C 173 "
           pdb=" N   PHE C 174 "
           pdb=" CA  PHE C 174 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.16  -16.84     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ILE D 173 "
           pdb=" C   ILE D 173 "
           pdb=" N   PHE D 174 "
           pdb=" CA  PHE D 174 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.22  -16.78     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 6705 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1498
       0.088 -    0.175: 101
       0.175 -    0.263: 21
       0.263 -    0.351: 16
       0.351 -    0.438: 16
  Chirality restraints: 1652
  Sorted by residual:
  chirality pdb=" C13 CLR D 401 "
            pdb=" C12 CLR D 401 "
            pdb=" C14 CLR D 401 "
            pdb=" C17 CLR D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.49   -0.44 2.00e-01 2.50e+01 4.81e+00
  chirality pdb=" C13 CLR B 401 "
            pdb=" C12 CLR B 401 "
            pdb=" C14 CLR B 401 "
            pdb=" C17 CLR B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.50   -0.44 2.00e-01 2.50e+01 4.74e+00
  chirality pdb=" C13 CLR A 405 "
            pdb=" C12 CLR A 405 "
            pdb=" C14 CLR A 405 "
            pdb=" C17 CLR A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.50   -0.44 2.00e-01 2.50e+01 4.73e+00
  ... (remaining 1649 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 156 "    0.011 2.00e-02 2.50e+03   2.09e-02 4.36e+00
        pdb=" C   VAL D 156 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL D 156 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TYR D 157 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 156 "    0.010 2.00e-02 2.50e+03   2.08e-02 4.33e+00
        pdb=" C   VAL A 156 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   VAL A 156 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TYR A 157 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 156 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.31e+00
        pdb=" C   VAL C 156 "    0.036 2.00e-02 2.50e+03
        pdb=" O   VAL C 156 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TYR C 157 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 135
        2.67 -     3.23: 9214
        3.23 -     3.78: 14422
        3.78 -     4.34: 18836
        4.34 -     4.90: 32234
  Nonbonded interactions: 74841
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 291 "
            pdb=" ND1 HIS B 294 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" O   ALA A 291 "
            pdb=" ND1 HIS A 294 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" O   ALA C 291 "
            pdb=" ND1 HIS C 294 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" O   ALA D 291 "
            pdb=" ND1 HIS D 294 "
     model   vdw
     2.110 3.120
  nonbonded pdb=" OE1 GLN B 272 "
            pdb=" NZ  LYS C  38 "
     model   vdw
     2.281 3.120
  ... (remaining 74836 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 26 through 404)
  selection = (chain 'B' and resid 26 through 404)
  selection = chain 'C'
  selection = (chain 'D' and resid 26 through 404)
}

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:             2.290
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.870
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
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      :  0.007   0.066   9940  Z= 0.338
  Angle     :  1.068  14.191  13676  Z= 0.462
  Chirality :  0.069   0.438   1652
  Planarity :  0.004   0.038   1536
  Dihedral  : 16.843  85.240   4532
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 16.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 30.36 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.26), residues: 1112
  helix:  1.95 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -2.78 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  77 
 TYR   0.007   0.001   TYR C 190 
 PHE   0.010   0.001   PHE B  49 
 TRP   0.011   0.001   TRP D  94 
 HIS   0.005   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 ( 9932)
  covalent geometry    : angle       1.06808 (13660)
  SS BOND              : bond        0.00169 (    8)
  SS BOND              : angle       1.10351 (   16)
  hydrogen bonds       : bond        0.11058 (  644)
  hydrogen bonds       : angle       6.31000 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.234 
Fit side-chains
  outliers start: 8
  outliers final: 5
  residues processed: 108
  average time/residue: 0.0671
  time to fit residues: 11.4232
Evaluate side-chains
  105 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain B residue   53 ILE
Chi-restraints excluded: chain C residue   53 ILE
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain D residue   53 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.5980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.172137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136239 restraints weight = 10445.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.65
r_work: 0.3548 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.0734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9940  Z= 0.164
  Angle     :  0.676   6.548  13676  Z= 0.330
  Chirality :  0.043   0.215   1652
  Planarity :  0.005   0.029   1536
  Dihedral  : 10.108  57.248   2518
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.51 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.27), residues: 1112
  helix:  1.89 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -2.82 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  77 
 TYR   0.008   0.001   TYR C 219 
 PHE   0.019   0.002   PHE C 264 
 TRP   0.015   0.002   TRP C 161 
 HIS   0.005   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9932)
  covalent geometry    : angle       0.67521 (13660)
  SS BOND              : bond        0.00016 (    8)
  SS BOND              : angle       0.94839 (   16)
  hydrogen bonds       : bond        0.06661 (  644)
  hydrogen bonds       : angle       5.71837 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 TYR cc_start: 0.6837 (m-80) cc_final: 0.6630 (m-80)
REVERT: A  179 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6398 (pm20)
REVERT: B  157 TYR cc_start: 0.6849 (m-80) cc_final: 0.6631 (m-80)
REVERT: B  179 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6398 (pm20)
REVERT: C  157 TYR cc_start: 0.6854 (m-80) cc_final: 0.6641 (m-80)
REVERT: C  179 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6390 (pm20)
REVERT: D  157 TYR cc_start: 0.6842 (m-80) cc_final: 0.6628 (m-80)
REVERT: D  179 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6404 (pm20)
  outliers start: 36
  outliers final: 16
  residues processed: 157
  average time/residue: 0.0711
  time to fit residues: 17.3411
Evaluate side-chains
  112 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0570
   chunk 2 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 90 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
B 106 ASN
C 106 ASN
D 106 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.176140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.140415 restraints weight = 10583.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3700 rms_B_bonded: 2.70
r_work: 0.3574 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9940  Z= 0.155
  Angle     :  0.619   6.057  13676  Z= 0.315
  Chirality :  0.042   0.167   1652
  Planarity :  0.005   0.034   1536
  Dihedral  :  9.467  58.573   2510
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 25.71 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.26), residues: 1112
  helix:  1.84 (0.19), residues: 792
  sheet:  None (None), residues: 0
  loop : -2.77 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  77 
 TYR   0.008   0.001   TYR C 103 
 PHE   0.034   0.002   PHE D  49 
 TRP   0.014   0.001   TRP C 161 
 HIS   0.004   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9932)
  covalent geometry    : angle       0.61855 (13660)
  SS BOND              : bond        0.00133 (    8)
  SS BOND              : angle       1.17762 (   16)
  hydrogen bonds       : bond        0.06402 (  644)
  hydrogen bonds       : angle       5.52670 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 104
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 TYR cc_start: 0.6746 (m-80) cc_final: 0.6449 (m-80)
REVERT: A  179 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6336 (pm20)
REVERT: A  253 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6973 (mp)
REVERT: B  157 TYR cc_start: 0.6744 (m-80) cc_final: 0.6438 (m-80)
REVERT: B  179 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6316 (pm20)
REVERT: B  253 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6970 (mp)
REVERT: C  157 TYR cc_start: 0.6751 (m-80) cc_final: 0.6442 (m-80)
REVERT: C  179 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6297 (pm20)
REVERT: C  253 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6988 (mp)
REVERT: D  157 TYR cc_start: 0.6761 (m-80) cc_final: 0.6448 (m-80)
REVERT: D  179 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6297 (pm20)
REVERT: D  253 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6975 (mp)
  outliers start: 44
  outliers final: 20
  residues processed: 136
  average time/residue: 0.0643
  time to fit residues: 14.4420
Evaluate side-chains
  119 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.164068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.127431 restraints weight = 10856.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 2.69
r_work: 0.3410 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.085   9940  Z= 0.260
  Angle     :  0.771   7.722  13676  Z= 0.389
  Chirality :  0.048   0.208   1652
  Planarity :  0.005   0.040   1536
  Dihedral  :  9.629  58.114   2510
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 24.19 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.26), residues: 1112
  helix:  1.56 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -2.69 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  77 
 TYR   0.015   0.002   TYR D 190 
 PHE   0.039   0.002   PHE D  49 
 TRP   0.014   0.002   TRP B 161 
 HIS   0.008   0.002   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 9932)
  covalent geometry    : angle       0.76970 (13660)
  SS BOND              : bond        0.00276 (    8)
  SS BOND              : angle       1.58834 (   16)
  hydrogen bonds       : bond        0.09078 (  644)
  hydrogen bonds       : angle       5.99219 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 104
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  179 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6356 (pm20)
REVERT: A  253 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7411 (mp)
REVERT: B  179 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6356 (pm20)
REVERT: B  253 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7415 (mp)
REVERT: C  179 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6351 (pm20)
REVERT: C  253 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7435 (mp)
REVERT: D  179 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6344 (pm20)
REVERT: D  253 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7419 (mp)
  outliers start: 51
  outliers final: 30
  residues processed: 138
  average time/residue: 0.0718
  time to fit residues: 15.6461
Evaluate side-chains
  132 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 94
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  280 VAL
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue   90 THR
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 83 optimal weight:    0.6980
   chunk 4 optimal weight:    8.9990
   chunk 16 optimal weight:    9.9990
   chunk 81 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.170709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.134499 restraints weight = 10708.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.70
r_work: 0.3505 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9940  Z= 0.170
  Angle     :  0.631   5.660  13676  Z= 0.332
  Chirality :  0.042   0.159   1652
  Planarity :  0.005   0.046   1536
  Dihedral  :  8.995  59.234   2510
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 25.81 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.26), residues: 1112
  helix:  1.84 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -2.78 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 134 
 TYR   0.019   0.001   TYR D 157 
 PHE   0.025   0.002   PHE D  49 
 TRP   0.011   0.002   TRP A 161 
 HIS   0.004   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9932)
  covalent geometry    : angle       0.62992 (13660)
  SS BOND              : bond        0.00168 (    8)
  SS BOND              : angle       1.34365 (   16)
  hydrogen bonds       : bond        0.07386 (  644)
  hydrogen bonds       : angle       5.66754 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 111
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6328 (pm20)
REVERT: A  253 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7303 (mp)
REVERT: B  179 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6325 (pm20)
REVERT: B  253 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7298 (mp)
REVERT: C  179 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6322 (pm20)
REVERT: C  253 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7323 (mp)
REVERT: D  179 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6314 (pm20)
REVERT: D  253 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7304 (mp)
  outliers start: 39
  outliers final: 24
  residues processed: 138
  average time/residue: 0.0719
  time to fit residues: 15.8856
Evaluate side-chains
  129 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 106 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.8786

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.169678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.133378 restraints weight = 10628.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 2.69
r_work: 0.3510 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9940  Z= 0.174
  Angle     :  0.632   5.348  13676  Z= 0.332
  Chirality :  0.042   0.152   1652
  Planarity :  0.005   0.048   1536
  Dihedral  :  8.537  58.334   2510
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.83 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 24.80 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.26), residues: 1112
  helix:  1.74 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -2.85 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  77 
 TYR   0.011   0.001   TYR B 157 
 PHE   0.025   0.002   PHE D  49 
 TRP   0.010   0.002   TRP B 161 
 HIS   0.005   0.001   HIS C 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 9932)
  covalent geometry    : angle       0.63075 (13660)
  SS BOND              : bond        0.00192 (    8)
  SS BOND              : angle       1.27695 (   16)
  hydrogen bonds       : bond        0.07214 (  644)
  hydrogen bonds       : angle       5.67519 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 112
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6301 (pm20)
REVERT: A  253 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7291 (mp)
REVERT: B  179 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6307 (pm20)
REVERT: B  253 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7313 (mp)
REVERT: C  179 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6287 (pm20)
REVERT: C  253 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7320 (mp)
REVERT: D  179 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6292 (pm20)
REVERT: D  253 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7264 (mp)
  outliers start: 46
  outliers final: 32
  residues processed: 139
  average time/residue: 0.0693
  time to fit residues: 15.3471
Evaluate side-chains
  148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 108
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 110 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.170736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.134836 restraints weight = 10592.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.64
r_work: 0.3528 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9940  Z= 0.168
  Angle     :  0.615   4.973  13676  Z= 0.321
  Chirality :  0.041   0.140   1652
  Planarity :  0.005   0.049   1536
  Dihedral  :  8.194  58.659   2510
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 25.20 %
    Favored  : 70.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.26), residues: 1112
  helix:  1.84 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -2.90 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  77 
 TYR   0.007   0.001   TYR A 219 
 PHE   0.022   0.001   PHE D  49 
 TRP   0.011   0.002   TRP D  94 
 HIS   0.005   0.001   HIS D 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9932)
  covalent geometry    : angle       0.61399 (13660)
  SS BOND              : bond        0.00173 (    8)
  SS BOND              : angle       1.30753 (   16)
  hydrogen bonds       : bond        0.07040 (  644)
  hydrogen bonds       : angle       5.60311 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 102
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6308 (pm20)
REVERT: A  253 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7298 (mp)
REVERT: B  179 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6311 (pm20)
REVERT: B  253 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7295 (mp)
REVERT: C  179 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6287 (pm20)
REVERT: C  253 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7263 (mp)
REVERT: D  179 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6290 (pm20)
REVERT: D  253 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7236 (mp)
  outliers start: 44
  outliers final: 33
  residues processed: 129
  average time/residue: 0.0749
  time to fit residues: 15.4035
Evaluate side-chains
  138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 97
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.4002 r_free = 0.4002 target = 0.169385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.133429 restraints weight = 10628.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.64
r_work: 0.3510 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9940  Z= 0.176
  Angle     :  0.636   7.310  13676  Z= 0.328
  Chirality :  0.042   0.142   1652
  Planarity :  0.005   0.050   1536
  Dihedral  :  8.148  59.273   2510
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 24.29 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.26), residues: 1112
  helix:  1.82 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -2.92 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  77 
 TYR   0.009   0.001   TYR D 157 
 PHE   0.025   0.002   PHE D  49 
 TRP   0.011   0.002   TRP D  94 
 HIS   0.006   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 9932)
  covalent geometry    : angle       0.63501 (13660)
  SS BOND              : bond        0.00200 (    8)
  SS BOND              : angle       1.36465 (   16)
  hydrogen bonds       : bond        0.07328 (  644)
  hydrogen bonds       : angle       5.63937 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 105
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6332 (pm20)
REVERT: A  253 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7334 (mp)
REVERT: B  179 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6335 (pm20)
REVERT: B  253 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7328 (mp)
REVERT: C  179 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6303 (pm20)
REVERT: C  253 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7357 (mp)
REVERT: D  179 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6291 (pm20)
REVERT: D  253 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7332 (mp)
  outliers start: 48
  outliers final: 35
  residues processed: 136
  average time/residue: 0.0702
  time to fit residues: 15.2729
Evaluate side-chains
  145 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 102
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  185 ILE
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue   39 ILE
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7762

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.171350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.135323 restraints weight = 10633.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.64
r_work: 0.3510 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9940  Z= 0.171
  Angle     :  0.636   5.955  13676  Z= 0.339
  Chirality :  0.042   0.140   1652
  Planarity :  0.005   0.050   1536
  Dihedral  :  7.973  59.449   2510
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.39 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.26), residues: 1112
  helix:  1.76 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -2.88 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  77 
 TYR   0.009   0.001   TYR A 157 
 PHE   0.022   0.001   PHE D  49 
 TRP   0.011   0.002   TRP D  94 
 HIS   0.004   0.001   HIS D 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9932)
  covalent geometry    : angle       0.63500 (13660)
  SS BOND              : bond        0.00142 (    8)
  SS BOND              : angle       1.19429 (   16)
  hydrogen bonds       : bond        0.07113 (  644)
  hydrogen bonds       : angle       5.58732 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 104
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6293 (pm20)
REVERT: A  253 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7198 (mp)
REVERT: B  179 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6298 (pm20)
REVERT: B  253 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7196 (mp)
REVERT: C  179 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6283 (pm20)
REVERT: C  253 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7214 (mp)
REVERT: D  179 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6273 (pm20)
REVERT: D  253 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7204 (mp)
  outliers start: 40
  outliers final: 31
  residues processed: 131
  average time/residue: 0.0688
  time to fit residues: 14.5873
Evaluate side-chains
  139 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 100
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  158 VAL
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  240 THR
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 110 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 40 optimal weight:    0.4980
   chunk 3 optimal weight:    2.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.173568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.137439 restraints weight = 10515.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 2.68
r_work: 0.3555 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9940  Z= 0.162
  Angle     :  0.615   5.908  13676  Z= 0.328
  Chirality :  0.041   0.137   1652
  Planarity :  0.005   0.050   1536
  Dihedral  :  7.686  59.551   2510
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.00 %
    Favored  : 71.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.26), residues: 1112
  helix:  1.82 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -2.93 (0.31), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 148 
 TYR   0.006   0.001   TYR A 103 
 PHE   0.024   0.001   PHE A  49 
 TRP   0.012   0.002   TRP A 161 
 HIS   0.004   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 9932)
  covalent geometry    : angle       0.61393 (13660)
  SS BOND              : bond        0.00129 (    8)
  SS BOND              : angle       1.23142 (   16)
  hydrogen bonds       : bond        0.06694 (  644)
  hydrogen bonds       : angle       5.50620 ( 1932)

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  179 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6250 (pm20)
REVERT: A  253 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7155 (mp)
REVERT: B  179 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6258 (pm20)
REVERT: B  253 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7151 (mp)
REVERT: C  179 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6253 (pm20)
REVERT: C  253 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7166 (mp)
REVERT: D  179 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6251 (pm20)
REVERT: D  253 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7146 (mp)
  outliers start: 36
  outliers final: 28
  residues processed: 136
  average time/residue: 0.0675
  time to fit residues: 14.7813
Evaluate side-chains
  136 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 ILE
Chi-restraints excluded: chain A residue   90 THR
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  179 GLU
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  279 THR
Chi-restraints excluded: chain A residue  293 PHE
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  179 GLU
Chi-restraints excluded: chain B residue  186 CYS
Chi-restraints excluded: chain B residue  240 THR
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  293 PHE
Chi-restraints excluded: chain B residue  294 HIS
Chi-restraints excluded: chain C residue   39 ILE
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  179 GLU
Chi-restraints excluded: chain C residue  186 CYS
Chi-restraints excluded: chain C residue  240 THR
Chi-restraints excluded: chain C residue  253 LEU
Chi-restraints excluded: chain C residue  279 THR
Chi-restraints excluded: chain C residue  293 PHE
Chi-restraints excluded: chain C residue  294 HIS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  179 GLU
Chi-restraints excluded: chain D residue  185 ILE
Chi-restraints excluded: chain D residue  186 CYS
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  279 THR
Chi-restraints excluded: chain D residue  293 PHE
Chi-restraints excluded: chain D residue  294 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 102 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.169169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133005 restraints weight = 10625.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.62
r_work: 0.3501 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9940  Z= 0.186
  Angle     :  0.660   6.677  13676  Z= 0.349
  Chirality :  0.043   0.141   1652
  Planarity :  0.005   0.050   1536
  Dihedral  :  7.940  58.992   2510
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.90 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1112
  helix:  1.70 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -2.91 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  77 
 TYR   0.012   0.001   TYR D 157 
 PHE   0.025   0.002   PHE D  49 
 TRP   0.011   0.002   TRP D  94 
 HIS   0.006   0.001   HIS D 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 9932)
  covalent geometry    : angle       0.65880 (13660)
  SS BOND              : bond        0.00223 (    8)
  SS BOND              : angle       1.35081 (   16)
  hydrogen bonds       : bond        0.07601 (  644)
  hydrogen bonds       : angle       5.67607 ( 1932)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1853.47 seconds
wall clock time: 32 minutes 40.81 seconds (1960.81 seconds total)