Starting phenix.real_space_refine
on Sat May 10 13:51:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgi_44513/05_2025/9bgi_44513.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgi_44513/05_2025/9bgi_44513.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.05
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bgi_44513/05_2025/9bgi_44513.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgi_44513/05_2025/9bgi_44513.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgi_44513/05_2025/9bgi_44513.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgi_44513/05_2025/9bgi_44513.cif"
  }
  resolution = 3.05
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.012 sd=   0.067
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: 6
    Type Number    sf(0)   Gaussians
     P      48      5.49       5
     Mg      4      5.21       5
     S      18      5.16       5
     C    3844      2.51       5
     N    1140      2.21       5
     O    1457      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6511
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 2672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2672
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 19, 'TRANS': 318}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 203
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "D"
      Number of atoms: 290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 290
          Classifications: {'DNA': 14}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "B"
      Number of atoms: 2672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2672
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 19, 'TRANS': 318}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 203
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "F"
      Number of atoms: 290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 290
          Classifications: {'DNA': 14}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 59
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 59
          Classifications: {'water': 59}
          Link IDs: {None: 58}
    Chain: "C"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "D"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 15
          Classifications: {'water': 15}
          Link IDs: {None: 14}
    Chain: "B"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 60
          Classifications: {'water': 60}
          Link IDs: {None: 59}
    Chain: "E"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
    Chain: "F"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 16
          Classifications: {'water': 16}
          Link IDs: {None: 15}
  Time building chain proxies: 4.68, per 1000 atoms: 0.72
  Number of scatterers: 6511
  At special positions: 0
  Unit cell: (84.66, 86.32, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      18     16.00
     P      48     15.00
     Mg      4     11.99
     O    1457      8.00
     N    1140      7.00
     C    3844      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 763.1 milliseconds
  

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1264

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      47.6% alpha, 7.7% beta
      22 base pairs and 42 stacking pairs defined.
    Time for finding SS restraints: 2.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 12
    Processing helix  chain 'A' and resid 38 through 47
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 63 through 68
    Processing helix  chain 'A' and resid 69 through 83
      removed outlier: 3.694A  pdb=" N   GLU A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 123
      removed outlier: 3.521A  pdb=" N   GLY A 123 " --> pdb=" O   SER A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 178
      removed outlier: 4.264A  pdb=" N   VAL A 167 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE A 168 " --> pdb=" O   SER A 164 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 199
      removed outlier: 3.621A  pdb=" N   GLN A 199 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 205
      removed outlier: 3.998A  pdb=" N   TRP A 204 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 221
    Processing helix  chain 'A' and resid 222 through 227
      removed outlier: 3.618A  pdb=" N   GLN A 227 " --> pdb=" O   GLN A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 233
      No H-bonds generated for 'chain 'A' and resid 231 through 233'
    Processing helix  chain 'A' and resid 250 through 266
      removed outlier: 3.935A  pdb=" N   LEU A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 291
    Processing helix  chain 'A' and resid 318 through 334
    Processing helix  chain 'B' and resid 6 through 12
    Processing helix  chain 'B' and resid 38 through 47
    Processing helix  chain 'B' and resid 56 through 61
    Processing helix  chain 'B' and resid 63 through 68
    Processing helix  chain 'B' and resid 69 through 83
    Processing helix  chain 'B' and resid 90 through 122
    Processing helix  chain 'B' and resid 140 through 143
    Processing helix  chain 'B' and resid 161 through 178
      removed outlier: 3.962A  pdb=" N   VAL B 167 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASP B 178 " --> pdb=" O   GLY B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 221
    Processing helix  chain 'B' and resid 223 through 227
    Processing helix  chain 'B' and resid 250 through 266
      removed outlier: 3.891A  pdb=" N   LEU B 254 " --> pdb=" O   LEU B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 291
      removed outlier: 3.536A  pdb=" N   THR B 290 " --> pdb=" O   ASN B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 334
    Processing helix  chain 'B' and resid 335 through 337
      No H-bonds generated for 'chain 'B' and resid 335 through 337'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149
      removed outlier: 7.133A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   ILE A 235 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   GLU A 276 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ALA A 238 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
      removed outlier: 7.596A  pdb=" N   HIS A 278 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ALA A 240 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
      removed outlier: 8.796A  pdb=" N   TYR A 314 " --> pdb=" O   PHE A 275 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL A 277 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22
    Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 148
      removed outlier: 7.185A  pdb=" N   VAL B 193 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ILE B 235 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU B 274 " --> pdb=" O   SER B 236 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU B 280 " --> pdb=" O   LYS B 242 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   SER B 244 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 8.667A  pdb=" N   TYR B 314 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   VAL B 277 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    645 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      57 hydrogen bonds
      114 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      42 stacking parallelities
  Total time for adding SS restraints: 2.01

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1564
        1.33 -     1.45: 1459
        1.45 -     1.57: 3417
        1.57 -     1.69: 92
        1.69 -     1.80: 32
  Bond restraints: 6564
  Sorted by residual:
  bond pdb=" N   ASP B  63 "
       pdb=" CA  ASP B  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.481 -0.025 1.23e-02 6.61e+03 4.05e+00
  bond pdb=" N   ASP A  63 "
       pdb=" CA  ASP A  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.479 -0.023 1.27e-02 6.20e+03 3.21e+00
  bond pdb=" C   GLN A 129 "
       pdb=" N   PRO A 130 "
    ideal  model  delta    sigma   weight residual
    1.333  1.349 -0.016 1.20e-02 6.94e+03 1.69e+00
  bond pdb=" C   ASP B  63 "
       pdb=" N   TYR B  64 "
    ideal  model  delta    sigma   weight residual
    1.335  1.319  0.016 1.38e-02 5.25e+03 1.34e+00
  bond pdb=" C4'  DT F  16 "
       pdb=" O4'  DT F  16 "
    ideal  model  delta    sigma   weight residual
    1.450  1.429  0.021 2.00e-02 2.50e+03 1.12e+00
  ... (remaining 6559 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 8907
        1.47 -     2.94: 167
        2.94 -     4.42: 26
        4.42 -     5.89: 7
        5.89 -     7.36: 1
  Bond angle restraints: 9108
  Sorted by residual:
  angle pdb=" N   ILE A  59 "
        pdb=" CA  ILE A  59 "
        pdb=" C   ILE A  59 "
      ideal   model   delta    sigma   weight residual
     112.96  108.92    4.04 1.00e+00 1.00e+00 1.63e+01
  angle pdb=" N   VAL B 122 "
        pdb=" CA  VAL B 122 "
        pdb=" C   VAL B 122 "
      ideal   model   delta    sigma   weight residual
     112.29  108.76    3.53 9.40e-01 1.13e+00 1.41e+01
  angle pdb=" CA  TRP B 156 "
        pdb=" CB  TRP B 156 "
        pdb=" CG  TRP B 156 "
      ideal   model   delta    sigma   weight residual
     113.60  118.45   -4.85 1.90e+00 2.77e-01 6.53e+00
  angle pdb=" C   ASP B 155 "
        pdb=" N   TRP B 156 "
        pdb=" CA  TRP B 156 "
      ideal   model   delta    sigma   weight residual
     121.54  126.39   -4.85 1.91e+00 2.74e-01 6.45e+00
  angle pdb=" CA  ASP A  63 "
        pdb=" C   ASP A  63 "
        pdb=" O   ASP A  63 "
      ideal   model   delta    sigma   weight residual
     121.15  118.56    2.59 1.10e+00 8.26e-01 5.53e+00
  ... (remaining 9103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3076
       17.70 -    35.41: 432
       35.41 -    53.11: 244
       53.11 -    70.82: 52
       70.82 -    88.52: 6
  Dihedral angle restraints: 3810
    sinusoidal: 1852
      harmonic: 1958
  Sorted by residual:
  dihedral pdb=" CA  GLN B 129 "
           pdb=" C   GLN B 129 "
           pdb=" N   PRO B 130 "
           pdb=" CA  PRO B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.83   23.17     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  GLN A 129 "
           pdb=" C   GLN A 129 "
           pdb=" N   PRO A 130 "
           pdb=" CA  PRO A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.91   23.09     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CB  GLU B 292 "
           pdb=" CG  GLU B 292 "
           pdb=" CD  GLU B 292 "
           pdb=" OE1 GLU B 292 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.52   88.52     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 3807 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 527
       0.024 -    0.048: 271
       0.048 -    0.072: 119
       0.072 -    0.096: 38
       0.096 -    0.120: 47
  Chirality restraints: 1002
  Sorted by residual:
  chirality pdb=" CA  ILE B  51 "
            pdb=" N   ILE B  51 "
            pdb=" C   ILE B  51 "
            pdb=" CB  ILE B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.61e-01
  chirality pdb=" CA  ILE A  68 "
            pdb=" N   ILE A  68 "
            pdb=" C   ILE A  68 "
            pdb=" CB  ILE A  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.42e-01
  chirality pdb=" CA  VAL A  28 "
            pdb=" N   VAL A  28 "
            pdb=" C   VAL A  28 "
            pdb=" CB  VAL A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.41e-01
  ... (remaining 999 not shown)

  Planarity restraints: 1032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 186 "    0.032 5.00e-02 4.00e+02   4.84e-02 3.74e+00
        pdb=" N   PRO B 187 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 187 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 187 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 129 "    0.023 5.00e-02 4.00e+02   3.51e-02 1.98e+00
        pdb=" N   PRO A 130 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 130 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 130 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 129 "    0.023 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO B 130 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B 130 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 130 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1029 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 117
        2.50 -     3.10: 4258
        3.10 -     3.70: 9785
        3.70 -     4.30: 15291
        4.30 -     4.90: 24863
  Nonbonded interactions: 54314
  Sorted by model distance:
  nonbonded pdb="MG    MG A 401 "
            pdb=" O   HOH C 105 "
     model   vdw
     1.899 2.170
  nonbonded pdb="MG    MG A 402 "
            pdb=" O   HOH A 515 "
     model   vdw
     1.918 2.170
  nonbonded pdb=" OP2  DC F  12 "
            pdb="MG    MG B 402 "
     model   vdw
     1.919 2.170
  nonbonded pdb="MG    MG B 401 "
            pdb=" O   HOH E 102 "
     model   vdw
     1.922 2.170
  nonbonded pdb=" OP2  DC D  12 "
            pdb="MG    MG A 402 "
     model   vdw
     1.926 2.170
  ... (remaining 54309 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.800
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6564  Z= 0.162
  Angle     :  0.523   7.362   9108  Z= 0.295
  Chirality :  0.040   0.120   1002
  Planarity :  0.004   0.048   1032
  Dihedral  : 20.545  88.520   2546
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.84 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.34), residues: 672
  helix:  1.39 (0.32), residues: 284
  sheet: -0.94 (0.69), residues: 54
  loop : -0.32 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 117 
 HIS   0.001   0.000   HIS A 278 
 PHE   0.009   0.001   PHE B   3 
 TYR   0.010   0.001   TYR B   5 
 ARG   0.002   0.000   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14871 (  281)
  hydrogen bonds       : angle       5.56149 (  759)
  covalent geometry    : bond        0.00362 ( 6564)
  covalent geometry    : angle       0.52307 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.625 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7685 (t80)
REVERT: A  200 ASN cc_start: 0.8969 (m-40) cc_final: 0.8748 (m-40)
REVERT: A  243 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.7806 (ttt-90)
REVERT: A  333 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7636 (tpt90)
REVERT: B  200 ASN cc_start: 0.8832 (m-40) cc_final: 0.8562 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 51
  average time/residue: 0.2473
  time to fit residues: 16.1304
Evaluate side-chains
  49 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   85 ASP
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  243 ARG
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    6.7992

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.133929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.100407 restraints weight = 7340.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.50
r_work: 0.3182 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.0947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.066   6564  Z= 0.317
  Angle     :  0.619   5.967   9108  Z= 0.333
  Chirality :  0.046   0.158   1002
  Planarity :  0.005   0.044   1032
  Dihedral  : 21.777  83.377   1285
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.67 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.34), residues: 672
  helix:  1.23 (0.31), residues: 288
  sheet: -1.19 (0.65), residues: 54
  loop : -0.25 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 117 
 HIS   0.003   0.001   HIS B  81 
 PHE   0.015   0.002   PHE B   3 
 TYR   0.020   0.002   TYR B   5 
 ARG   0.005   0.001   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06185 (  281)
  hydrogen bonds       : angle       4.28238 (  759)
  covalent geometry    : bond        0.00762 ( 6564)
  covalent geometry    : angle       0.61872 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8319 (t80)
REVERT: A  333 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7723 (tpt90)
REVERT: B  169 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7878 (mm-30)
REVERT: B  200 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8427 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 54
  average time/residue: 0.2251
  time to fit residues: 16.0299
Evaluate side-chains
  51 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  297 TYR
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 49 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:   20.0000
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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 = 0.3860 r_free = 0.3860 target = 0.139274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.106045 restraints weight = 7380.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.49
r_work: 0.3263 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6564  Z= 0.134
  Angle     :  0.491   5.331   9108  Z= 0.266
  Chirality :  0.039   0.128   1002
  Planarity :  0.004   0.039   1032
  Dihedral  : 21.424  85.142   1275
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.02 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.34), residues: 672
  helix:  1.72 (0.32), residues: 288
  sheet: -0.63 (0.73), residues: 48
  loop : -0.06 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 156 
 HIS   0.001   0.000   HIS A 278 
 PHE   0.007   0.001   PHE B   3 
 TYR   0.009   0.001   TYR A   5 
 ARG   0.002   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04118 (  281)
  hydrogen bonds       : angle       3.77050 (  759)
  covalent geometry    : bond        0.00309 ( 6564)
  covalent geometry    : angle       0.49145 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8441 (t80)
REVERT: A  260 MET cc_start: 0.9001 (ttm) cc_final: 0.8772 (ttt)
REVERT: A  333 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7682 (tpt90)
REVERT: B  169 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7909 (mm-30)
REVERT: B  176 ARG cc_start: 0.8387 (mmm160) cc_final: 0.7943 (tpt90)
REVERT: B  200 ASN cc_start: 0.8844 (m-40) cc_final: 0.8443 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 56
  average time/residue: 0.2196
  time to fit residues: 16.3757
Evaluate side-chains
  50 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   36 GLN
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 16 optimal weight:    8.9990
   chunk 23 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.134369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.100671 restraints weight = 7436.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 1.52
r_work: 0.3182 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8870
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   6564  Z= 0.276
  Angle     :  0.584   5.543   9108  Z= 0.313
  Chirality :  0.045   0.141   1002
  Planarity :  0.005   0.039   1032
  Dihedral  : 21.632  82.286   1275
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.07 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.34), residues: 672
  helix:  1.49 (0.31), residues: 288
  sheet: -1.09 (0.67), residues: 52
  loop : -0.13 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 156 
 HIS   0.002   0.001   HIS B  81 
 PHE   0.012   0.002   PHE B   3 
 TYR   0.018   0.002   TYR B   5 
 ARG   0.004   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05574 (  281)
  hydrogen bonds       : angle       3.97794 (  759)
  covalent geometry    : bond        0.00665 ( 6564)
  covalent geometry    : angle       0.58367 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8316 (t80)
REVERT: A  333 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7819 (tpt90)
REVERT: B  200 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8431 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 56
  average time/residue: 0.2202
  time to fit residues: 16.2503
Evaluate side-chains
  53 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain A residue  297 TYR
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 69 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.136604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.103314 restraints weight = 7404.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.48
r_work: 0.3217 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6564  Z= 0.180
  Angle     :  0.519   5.421   9108  Z= 0.280
  Chirality :  0.041   0.126   1002
  Planarity :  0.004   0.035   1032
  Dihedral  : 21.403  82.686   1272
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.67 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.34), residues: 672
  helix:  1.69 (0.32), residues: 288
  sheet: -1.04 (0.68), residues: 52
  loop : -0.06 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 156 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.009   0.001   PHE B   3 
 TYR   0.012   0.001   TYR A   5 
 ARG   0.003   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04584 (  281)
  hydrogen bonds       : angle       3.76033 (  759)
  covalent geometry    : bond        0.00429 ( 6564)
  covalent geometry    : angle       0.51858 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.617 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8375 (t80)
REVERT: A  333 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7772 (tpt90)
REVERT: B  200 ASN cc_start: 0.8815 (m-40) cc_final: 0.8554 (t0)
REVERT: B  229 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8215 (mmt-90)
  outliers start: 17
  outliers final: 12
  residues processed: 55
  average time/residue: 0.2184
  time to fit residues: 15.7174
Evaluate side-chains
  53 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  203 MET
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 65 optimal weight:   10.0000
   chunk 40 optimal weight:    0.0020
   chunk 61 optimal weight:    0.0040
   chunk 30 optimal weight:    0.0000
   chunk 47 optimal weight:   20.0000
   chunk 28 optimal weight:    0.0870
   chunk 25 optimal weight:    5.9990
   chunk 35 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3902 r_free = 0.3902 target = 0.142006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.109500 restraints weight = 7232.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.46
r_work: 0.3338 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6564  Z= 0.111
  Angle     :  0.468   5.388   9108  Z= 0.252
  Chirality :  0.038   0.130   1002
  Planarity :  0.003   0.034   1032
  Dihedral  : 21.250  83.293   1272
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.67 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.35), residues: 672
  helix:  2.02 (0.32), residues: 288
  sheet: -0.33 (0.73), residues: 58
  loop :  0.11 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 156 
 HIS   0.000   0.000   HIS B 307 
 PHE   0.004   0.001   PHE B   3 
 TYR   0.008   0.001   TYR B   5 
 ARG   0.002   0.000   ARG A  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  281)
  hydrogen bonds       : angle       3.48826 (  759)
  covalent geometry    : bond        0.00248 ( 6564)
  covalent geometry    : angle       0.46843 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.626 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8500 (t80)
REVERT: A  333 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7817 (tpt90)
REVERT: B  169 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7984 (mm-30)
REVERT: B  176 ARG cc_start: 0.8296 (mmm160) cc_final: 0.7918 (tpt90)
REVERT: B  200 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8554 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 57
  average time/residue: 0.2006
  time to fit residues: 15.2482
Evaluate side-chains
  54 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    8.9990
   chunk 50 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0570
   chunk 64 optimal weight:    8.9990
   chunk 30 optimal weight:   20.0000
   chunk 56 optimal weight:    0.9980
   overall best weight:    2.9902

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.138351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.105066 restraints weight = 7268.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.47
r_work: 0.3255 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6564  Z= 0.166
  Angle     :  0.505   6.499   9108  Z= 0.271
  Chirality :  0.040   0.128   1002
  Planarity :  0.004   0.034   1032
  Dihedral  : 21.286  81.622   1272
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.67 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.34), residues: 672
  helix:  1.89 (0.32), residues: 288
  sheet: -0.81 (0.72), residues: 48
  loop :  0.09 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 156 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.007   0.001   PHE B   3 
 TYR   0.018   0.001   TYR B   5 
 ARG   0.003   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  281)
  hydrogen bonds       : angle       3.59563 (  759)
  covalent geometry    : bond        0.00392 ( 6564)
  covalent geometry    : angle       0.50455 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8977 (OUTLIER) cc_final: 0.8451 (t80)
REVERT: A  333 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7800 (tpt90)
REVERT: B  200 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8534 (t0)
REVERT: B  229 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8163 (mmt-90)
  outliers start: 18
  outliers final: 13
  residues processed: 57
  average time/residue: 0.2267
  time to fit residues: 16.9655
Evaluate side-chains
  56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 53 optimal weight:    0.4980
   chunk 12 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 261 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.140242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.107090 restraints weight = 7251.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.48
r_work: 0.3291 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6564  Z= 0.133
  Angle     :  0.486   6.543   9108  Z= 0.260
  Chirality :  0.039   0.127   1002
  Planarity :  0.003   0.034   1032
  Dihedral  : 21.219  81.469   1272
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.84 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.34), residues: 672
  helix:  1.99 (0.32), residues: 290
  sheet: -0.79 (0.72), residues: 48
  loop :  0.15 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 156 
 HIS   0.001   0.000   HIS B 307 
 PHE   0.007   0.001   PHE B   3 
 TYR   0.014   0.001   TYR B   5 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  281)
  hydrogen bonds       : angle       3.50800 (  759)
  covalent geometry    : bond        0.00310 ( 6564)
  covalent geometry    : angle       0.48569 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8434 (t80)
REVERT: A  333 ARG cc_start: 0.8117 (mmm-85) cc_final: 0.7812 (tpt90)
REVERT: B  169 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7895 (mm-30)
REVERT: B  176 ARG cc_start: 0.8370 (mmm160) cc_final: 0.7931 (tpt90)
REVERT: B  200 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8531 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 57
  average time/residue: 0.2436
  time to fit residues: 18.3161
Evaluate side-chains
  57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 3 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.136006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.102445 restraints weight = 7438.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 1.49
r_work: 0.3207 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8844
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6564  Z= 0.205
  Angle     :  0.537   6.359   9108  Z= 0.288
  Chirality :  0.042   0.135   1002
  Planarity :  0.004   0.033   1032
  Dihedral  : 21.349  79.966   1272
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.84 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.34), residues: 672
  helix:  1.77 (0.32), residues: 288
  sheet: -1.05 (0.67), residues: 52
  loop :  0.04 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 117 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.009   0.001   PHE B   3 
 TYR   0.022   0.002   TYR B   5 
 ARG   0.003   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04854 (  281)
  hydrogen bonds       : angle       3.71311 (  759)
  covalent geometry    : bond        0.00490 ( 6564)
  covalent geometry    : angle       0.53706 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8403 (t80)
REVERT: A  333 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7821 (tpt90)
REVERT: B  200 ASN cc_start: 0.8834 (OUTLIER) cc_final: 0.8555 (t0)
REVERT: B  229 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8088 (mmt-90)
  outliers start: 17
  outliers final: 13
  residues processed: 53
  average time/residue: 0.2315
  time to fit residues: 16.0691
Evaluate side-chains
  55 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 52 optimal weight:    8.9990
   overall best weight:    2.7986

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.137198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.103561 restraints weight = 7469.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.54
r_work: 0.3227 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6564  Z= 0.159
  Angle     :  0.504   6.277   9108  Z= 0.271
  Chirality :  0.040   0.124   1002
  Planarity :  0.004   0.033   1032
  Dihedral  : 21.261  80.063   1272
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.02 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.34), residues: 672
  helix:  1.87 (0.32), residues: 288
  sheet: -0.78 (0.73), residues: 48
  loop :  0.13 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 156 
 HIS   0.001   0.000   HIS B  81 
 PHE   0.007   0.001   PHE B   3 
 TYR   0.017   0.001   TYR B   5 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04296 (  281)
  hydrogen bonds       : angle       3.60261 (  759)
  covalent geometry    : bond        0.00376 ( 6564)
  covalent geometry    : angle       0.50436 ( 9108)

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

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

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1344 Ramachandran restraints generated.
    672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.678 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8460 (t80)
REVERT: A  333 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7859 (tpt90)
REVERT: B  121 MET cc_start: 0.7684 (mtp) cc_final: 0.7399 (mtp)
REVERT: B  200 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8545 (t0)
REVERT: B  229 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8088 (mmt-90)
  outliers start: 16
  outliers final: 13
  residues processed: 55
  average time/residue: 0.2258
  time to fit residues: 16.3660
Evaluate side-chains
  55 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 THR
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  184 THR
Chi-restraints excluded: chain B residue   39 GLN
Chi-restraints excluded: chain B residue   64 TYR
Chi-restraints excluded: chain B residue   91 SER
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  200 ASN
Chi-restraints excluded: chain B residue  229 ARG
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  297 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 55 optimal weight:   20.0000
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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 = 0.3886 r_free = 0.3886 target = 0.141531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.108111 restraints weight = 7516.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.56
r_work: 0.3287 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6564  Z= 0.109
  Angle     :  0.472   6.030   9108  Z= 0.253
  Chirality :  0.038   0.130   1002
  Planarity :  0.003   0.034   1032
  Dihedral  : 21.134  80.481   1272
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.38 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.35), residues: 672
  helix:  2.07 (0.32), residues: 290
  sheet: -0.25 (0.74), residues: 58
  loop :  0.20 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 156 
 HIS   0.000   0.000   HIS B 307 
 PHE   0.004   0.001   PHE B   3 
 TYR   0.009   0.001   TYR B   5 
 ARG   0.002   0.000   ARG B 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03462 (  281)
  hydrogen bonds       : angle       3.44854 (  759)
  covalent geometry    : bond        0.00244 ( 6564)
  covalent geometry    : angle       0.47207 ( 9108)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3388.97 seconds
wall clock time: 59 minutes 20.90 seconds (3560.90 seconds total)