Starting phenix.real_space_refine
on Sun Apr 27 18:41:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgi_44513/04_2025/9bgi_44513.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgi_44513/04_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_44513/04_2025/9bgi_44513.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgi_44513/04_2025/9bgi_44513.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgi_44513/04_2025/9bgi_44513.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgi_44513/04_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-5669/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: 5.15, per 1000 atoms: 0.79
  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: 1.74
  Conformation dependent library (CDL) restraints added in 856.4 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: 2.36
  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: 2.13

  Time building geometry restraints manager: 2.04 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:             1.440
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.860
  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:             0.010
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.950
-------------------------------------------------------------------------------
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  : 0.719 
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: 0.2761
  time to fit residues: 17.9780
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  : 0.722 
-------------------------------------------------------------------------------
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 = 46)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.100410 restraints weight = 7340.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 1.50
r_work: 0.3180 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
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  : 0.636 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8318 (t80)
REVERT: A  333 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7714 (tpt90)
REVERT: B  169 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7873 (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: 0.2203
  time to fit residues: 15.7287
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  : 0.759 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.139088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.105874 restraints weight = 7375.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.49
r_work: 0.3256 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.0853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6564  Z= 0.132
  Angle     :  0.493   5.331   9108  Z= 0.267
  Chirality :  0.039   0.127   1002
  Planarity :  0.004   0.039   1032
  Dihedral  : 21.440  85.078   1275
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  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:  0.88 (0.34), residues: 672
  helix:  1.72 (0.32), residues: 288
  sheet: -0.87 (0.68), residues: 52
  loop : -0.13 (0.37), residues: 332

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        0.04177 (  281)
  hydrogen bonds       : angle       3.79435 (  759)
  covalent geometry    : bond        0.00302 ( 6564)
  covalent geometry    : angle       0.49304 ( 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
  57 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.679 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.8345 (t80)
REVERT: A  333 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7671 (tpt90)
REVERT: B  169 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7894 (mm-30)
REVERT: B  176 ARG cc_start: 0.8386 (mmm160) cc_final: 0.7937 (tpt90)
REVERT: B  200 ASN cc_start: 0.8862 (m-40) cc_final: 0.8459 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 55
  average time/residue: 0.2123
  time to fit residues: 15.5921
Evaluate side-chains
  49 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 16 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.133979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100514 restraints weight = 7441.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.50
r_work: 0.3177 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.1084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061   6564  Z= 0.284
  Angle     :  0.591   5.543   9108  Z= 0.318
  Chirality :  0.045   0.143   1002
  Planarity :  0.005   0.039   1032
  Dihedral  : 21.662  82.146   1275
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.25 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.34), residues: 672
  helix:  1.47 (0.31), residues: 288
  sheet: -1.34 (0.65), residues: 54
  loop : -0.10 (0.37), residues: 330

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        0.05684 (  281)
  hydrogen bonds       : angle       4.00140 (  759)
  covalent geometry    : bond        0.00685 ( 6564)
  covalent geometry    : angle       0.59137 ( 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  : 0.643 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8319 (t80)
REVERT: A  333 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7807 (tpt90)
REVERT: B  200 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8444 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 57
  average time/residue: 0.2219
  time to fit residues: 16.7991
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  : 0.634 
-------------------------------------------------------------------------------
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  161 VAL
Chi-restraints excluded: chain A residue  167 VAL
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:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3881 r_free = 0.3881 target = 0.140286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.107224 restraints weight = 7286.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.48
r_work: 0.3295 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6564  Z= 0.127
  Angle     :  0.487   5.340   9108  Z= 0.263
  Chirality :  0.039   0.125   1002
  Planarity :  0.004   0.035   1032
  Dihedral  : 21.333  83.778   1272
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  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:  1.11 (0.35), residues: 672
  helix:  1.86 (0.32), residues: 288
  sheet: -0.76 (0.73), residues: 48
  loop :  0.04 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 156 
 HIS   0.000   0.000   HIS B 307 
 PHE   0.006   0.001   PHE B   3 
 TYR   0.008   0.001   TYR A   5 
 ARG   0.002   0.000   ARG B 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  281)
  hydrogen bonds       : angle       3.64164 (  759)
  covalent geometry    : bond        0.00291 ( 6564)
  covalent geometry    : angle       0.48749 ( 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
  58 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8456 (t80)
REVERT: A  260 MET cc_start: 0.8953 (ttm) cc_final: 0.8744 (ttt)
REVERT: A  333 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7767 (tpt90)
REVERT: B  176 ARG cc_start: 0.8325 (mmm160) cc_final: 0.7922 (tpt90)
REVERT: B  200 ASN cc_start: 0.8807 (m-40) cc_final: 0.8553 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 55
  average time/residue: 0.2073
  time to fit residues: 15.2550
Evaluate side-chains
  54 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
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  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:   20.0000
   chunk 40 optimal weight:    0.0010
   chunk 61 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 35 optimal weight:   10.0000
   chunk 57 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    2.1592

-------------------------------------------------------------------------------
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 = 0.3874 r_free = 0.3874 target = 0.139655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.106521 restraints weight = 7223.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.47
r_work: 0.3281 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.1076

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= 0.139
  Angle     :  0.485   5.362   9108  Z= 0.260
  Chirality :  0.040   0.129   1002
  Planarity :  0.004   0.034   1032
  Dihedral  : 21.287  82.480   1272
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.96 %
    Favored  : 81.03 %
  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:  1.91 (0.32), residues: 288
  sheet: -0.76 (0.73), residues: 48
  loop :  0.07 (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 B 307 
 PHE   0.007   0.001   PHE B   3 
 TYR   0.008   0.001   TYR B   5 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04010 (  281)
  hydrogen bonds       : angle       3.56925 (  759)
  covalent geometry    : bond        0.00323 ( 6564)
  covalent geometry    : angle       0.48467 ( 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
  58 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8439 (t80)
REVERT: A  260 MET cc_start: 0.8963 (ttm) cc_final: 0.8744 (ttt)
REVERT: A  333 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7807 (tpt90)
REVERT: B  169 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7884 (mm-30)
REVERT: B  176 ARG cc_start: 0.8353 (mmm160) cc_final: 0.7919 (tpt90)
REVERT: B  200 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8550 (t0)
REVERT: B  229 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8194 (mmt-90)
  outliers start: 17
  outliers final: 12
  residues processed: 54
  average time/residue: 0.2306
  time to fit residues: 16.3818
Evaluate side-chains
  54 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
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  200 ASN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 16 optimal weight:    8.9990
   chunk 11 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 50 optimal weight:    8.9990
   chunk 21 optimal weight:    0.4980
   chunk 64 optimal weight:   20.0000
   chunk 30 optimal weight:    0.0980
   chunk 56 optimal weight:    2.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.138799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.105468 restraints weight = 7264.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.48
r_work: 0.3262 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.1082

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= 0.156
  Angle     :  0.494   5.342   9108  Z= 0.265
  Chirality :  0.040   0.127   1002
  Planarity :  0.004   0.033   1032
  Dihedral  : 21.288  81.800   1272
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.96 %
    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:  1.15 (0.34), residues: 672
  helix:  1.90 (0.32), residues: 288
  sheet: -0.79 (0.73), residues: 48
  loop :  0.08 (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 307 
 PHE   0.007   0.001   PHE B   3 
 TYR   0.010   0.001   TYR A   5 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04249 (  281)
  hydrogen bonds       : angle       3.61881 (  759)
  covalent geometry    : bond        0.00368 ( 6564)
  covalent geometry    : angle       0.49430 ( 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: 19
    poor density    : 41
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8459 (t80)
REVERT: A  333 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.7810 (tpt90)
REVERT: B  176 ARG cc_start: 0.8400 (mmm160) cc_final: 0.7952 (tpt90)
REVERT: B  200 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8535 (t0)
REVERT: B  229 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8195 (mmt-90)
  outliers start: 19
  outliers final: 14
  residues processed: 56
  average time/residue: 0.2279
  time to fit residues: 16.8052
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  : 0.671 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 52 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 53 optimal weight:    0.1980
   chunk 12 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.139292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.106190 restraints weight = 7240.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.46
r_work: 0.3279 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.1142

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= 0.144
  Angle     :  0.485   5.315   9108  Z= 0.261
  Chirality :  0.040   0.128   1002
  Planarity :  0.004   0.034   1032
  Dihedral  : 21.244  81.416   1272
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.78 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.23 (0.34), residues: 672
  helix:  1.95 (0.32), residues: 288
  sheet: -0.77 (0.73), residues: 48
  loop :  0.15 (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 B 307 
 PHE   0.007   0.001   PHE B   3 
 TYR   0.009   0.001   TYR A   5 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  281)
  hydrogen bonds       : angle       3.56131 (  759)
  covalent geometry    : bond        0.00338 ( 6564)
  covalent geometry    : angle       0.48543 ( 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: 19
    poor density    : 42
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8440 (t80)
REVERT: A  260 MET cc_start: 0.8968 (ttm) cc_final: 0.8739 (ttt)
REVERT: A  333 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7774 (tpt90)
REVERT: B  176 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7934 (tpt90)
REVERT: B  200 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8528 (t0)
REVERT: B  229 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8068 (mmt-90)
  outliers start: 19
  outliers final: 13
  residues processed: 56
  average time/residue: 0.2295
  time to fit residues: 17.0565
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  : 0.625 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   chunk 58 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 55 optimal weight:   20.0000
   chunk 0 optimal weight:    8.9990
   chunk 3 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    3.5588

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.137517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.104180 restraints weight = 7338.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.47
r_work: 0.3242 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6564  Z= 0.186
  Angle     :  0.517   5.399   9108  Z= 0.276
  Chirality :  0.041   0.127   1002
  Planarity :  0.004   0.033   1032
  Dihedral  : 21.317  80.301   1272
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.31 %
    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:  1.05 (0.34), residues: 672
  helix:  1.82 (0.32), residues: 288
  sheet: -1.03 (0.68), residues: 52
  loop :  0.06 (0.37), residues: 332

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   0.008   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        0.04597 (  281)
  hydrogen bonds       : angle       3.67640 (  759)
  covalent geometry    : bond        0.00444 ( 6564)
  covalent geometry    : angle       0.51663 ( 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  : 0.754 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8373 (t80)
REVERT: A  333 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7831 (tpt90)
REVERT: B  200 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8528 (t0)
REVERT: B  229 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8105 (mmt-90)
  outliers start: 17
  outliers final: 14
  residues processed: 53
  average time/residue: 0.3133
  time to fit residues: 21.7053
Evaluate side-chains
  55 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 38
  time to evaluate  : 1.286 
-------------------------------------------------------------------------------
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   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:    0.7980
   chunk 40 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.139434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.106187 restraints weight = 7356.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.48
r_work: 0.3274 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.1182

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= 0.143
  Angle     :  0.490   5.578   9108  Z= 0.262
  Chirality :  0.040   0.126   1002
  Planarity :  0.004   0.034   1032
  Dihedral  : 21.226  80.404   1272
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 16.49 %
    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:  1.31 (0.35), residues: 672
  helix:  1.96 (0.32), residues: 288
  sheet: -0.34 (0.73), residues: 58
  loop :  0.19 (0.38), residues: 326

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   0.006   0.001   PHE B   3 
 TYR   0.009   0.001   TYR A   5 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  281)
  hydrogen bonds       : angle       3.56510 (  759)
  covalent geometry    : bond        0.00336 ( 6564)
  covalent geometry    : angle       0.49004 ( 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
  58 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 41
  time to evaluate  : 1.324 
Fit side-chains
REVERT: A   64 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8444 (t80)
REVERT: A  333 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7798 (tpt90)
REVERT: B  200 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8526 (t0)
REVERT: B  229 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8091 (mmt-90)
  outliers start: 17
  outliers final: 13
  residues processed: 55
  average time/residue: 0.3040
  time to fit residues: 23.1878
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  : 1.600 
-------------------------------------------------------------------------------
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 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:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.139922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.106739 restraints weight = 7386.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.49
r_work: 0.3282 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6564  Z= 0.138
  Angle     :  0.484   5.341   9108  Z= 0.259
  Chirality :  0.039   0.129   1002
  Planarity :  0.003   0.034   1032
  Dihedral  : 21.180  79.783   1272
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.84 %
    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:  1.37 (0.35), residues: 672
  helix:  2.01 (0.32), residues: 288
  sheet: -0.32 (0.73), residues: 58
  loop :  0.22 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 156 
 HIS   0.001   0.000   HIS B 307 
 PHE   0.006   0.001   PHE B   3 
 TYR   0.009   0.001   TYR B   5 
 ARG   0.002   0.000   ARG B  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03946 (  281)
  hydrogen bonds       : angle       3.53303 (  759)
  covalent geometry    : bond        0.00321 ( 6564)
  covalent geometry    : angle       0.48383 ( 9108)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4023.53 seconds
wall clock time: 71 minutes 16.73 seconds (4276.73 seconds total)