Starting phenix.real_space_refine
on Wed Sep 17 11:48:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mue_48630/09_2025/9mue_48630.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mue_48630/09_2025/9mue_48630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mue_48630/09_2025/9mue_48630.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mue_48630/09_2025/9mue_48630.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mue_48630/09_2025/9mue_48630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mue_48630/09_2025/9mue_48630.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.050
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      20      5.16       5
     C    5434      2.51       5
     N    1430      2.21       5
     O    1542      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8438
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "a"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "b"
      Number of atoms: 88
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 88
          Classifications: {'RNA': 4}
          Modifications used: {'rna2p_pur': 4}
          Link IDs: {'rna2p': 3}
    Chain: "B"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 2022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2022
          Classifications: {'peptide': 249}
          Link IDs: {'PTRANS': 12, 'TRANS': 236}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2073
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2073
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 13, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'AR6': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'AR6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.21, per 1000 atoms: 0.26
  Number of scatterers: 8438
  At special positions: 0
  Unit cell: (65.912, 130.112, 83.888, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P      12     15.00
     O    1542      8.00
     N    1430      7.00
     C    5434      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: 0.73
  Conformation dependent library (CDL) restraints added in 404.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 10 sheets defined
      36.8% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 11
      No H-bonds generated for 'chain 'A' and resid 9 through 11'
    Processing helix  chain 'A' and resid 12 through 25
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 96 through 100
    Processing helix  chain 'A' and resid 106 through 119
    Processing helix  chain 'A' and resid 129 through 142
    Processing helix  chain 'A' and resid 177 through 182
      removed outlier: 4.053A  pdb=" N   HIS A 181 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 190
      removed outlier: 4.090A  pdb=" N   ASP A 188 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ILE A 190 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 222
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'B' and resid 9 through 11
      No H-bonds generated for 'chain 'B' and resid 9 through 11'
    Processing helix  chain 'B' and resid 12 through 25
      removed outlier: 3.557A  pdb=" N   GLU B  18 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 83
      removed outlier: 3.666A  pdb=" N   TRP B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   GLU B  74 " --> pdb=" O   TRP B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 100
    Processing helix  chain 'B' and resid 106 through 120
    Processing helix  chain 'B' and resid 129 through 144
      removed outlier: 4.635A  pdb=" N   ASN B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 182
      removed outlier: 4.096A  pdb=" N   HIS B 181 " --> pdb=" O   ASP B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 190
      removed outlier: 3.570A  pdb=" N   ASP B 188 " --> pdb=" O   LYS B 185 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ILE B 190 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
    Processing helix  chain 'B' and resid 223 through 225
      No H-bonds generated for 'chain 'B' and resid 223 through 225'
    Processing helix  chain 'C' and resid 12 through 25
    Processing helix  chain 'C' and resid 64 through 67
    Processing helix  chain 'C' and resid 68 through 83
      removed outlier: 5.028A  pdb=" N   GLU C  74 " --> pdb=" O   TRP C  70 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU C  75 " --> pdb=" O   CYS C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 100
      removed outlier: 3.774A  pdb=" N   LEU C 100 " --> pdb=" O   ARG C  97 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 120
    Processing helix  chain 'C' and resid 129 through 142
    Processing helix  chain 'C' and resid 177 through 182
      removed outlier: 3.564A  pdb=" N   TRP C 182 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 190
      removed outlier: 3.903A  pdb=" N   ASP C 188 " --> pdb=" O   LYS C 185 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE C 190 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 222
    Processing helix  chain 'C' and resid 223 through 225
      No H-bonds generated for 'chain 'C' and resid 223 through 225'
    Processing helix  chain 'D' and resid 9 through 11
      No H-bonds generated for 'chain 'D' and resid 9 through 11'
    Processing helix  chain 'D' and resid 12 through 25
      removed outlier: 3.625A  pdb=" N   GLU D  18 " --> pdb=" O   LYS D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 48
    Processing helix  chain 'D' and resid 68 through 83
      removed outlier: 3.897A  pdb=" N   TRP D  72 " --> pdb=" O   SER D  68 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ASP D  73 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   GLU D  74 " --> pdb=" O   TRP D  70 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 100
    Processing helix  chain 'D' and resid 106 through 120
    Processing helix  chain 'D' and resid 129 through 143
    Processing helix  chain 'D' and resid 177 through 182
      removed outlier: 3.681A  pdb=" N   TRP D 182 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 190
    Processing helix  chain 'D' and resid 213 through 222
    Processing helix  chain 'D' and resid 223 through 225
      No H-bonds generated for 'chain 'D' and resid 223 through 225'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31
      removed outlier: 3.706A  pdb=" N   PHE A   6 " --> pdb=" O   TRP A  31 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A   5 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LYS A  88 " --> pdb=" O   GLN A  55 " (cutoff:3.500A)
      removed outlier: 8.606A  pdb=" N   VAL A 123 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 157
      removed outlier: 4.037A  pdb=" N   GLU A 166 " --> pdb=" O   GLU A 150 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ILE A 152 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   VAL A 164 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   MET A 154 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU A 162 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   LYS A 156 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 5.579A  pdb=" N   THR A 160 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ALA A 207 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   GLN A 163 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   TYR A 209 " --> pdb=" O   GLN A 163 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL A 165 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   VAL A 206 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   PHE A 233 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   LEU A 208 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31
      removed outlier: 4.106A  pdb=" N   PHE B   5 " --> pdb=" O   TYR B  56 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   PHE B  57 " --> pdb=" O   ILE B  90 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ILE B  92 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   ALA B  59 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 157
      removed outlier: 5.272A  pdb=" N   GLU B 166 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ARG B 153 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   VAL B 206 " --> pdb=" O   PHE B 231 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   PHE B 233 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      removed outlier: 7.103A  pdb=" N   LEU B 208 " --> pdb=" O   PHE B 233 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLU B 239 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 31
      removed outlier: 6.148A  pdb=" N   ALA C   4 " --> pdb=" O   TRP C  31 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   GLN C   3 " --> pdb=" O   TYR C  56 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   LEU C  58 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   PHE C   5 " --> pdb=" O   LEU C  58 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   PHE C  60 " --> pdb=" O   PHE C   5 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   SER C   7 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LYS C  88 " --> pdb=" O   GLN C  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 150 through 157
      removed outlier: 5.339A  pdb=" N   GLU C 166 " --> pdb=" O   PRO C 151 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ARG C 153 " --> pdb=" O   VAL C 164 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   ALA C 207 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   GLN C 163 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   TYR C 209 " --> pdb=" O   GLN C 163 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   VAL C 165 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   VAL C 206 " --> pdb=" O   PHE C 231 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   PHE C 233 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   LEU C 208 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.267A  pdb=" N   ALA D   4 " --> pdb=" O   TRP D  31 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   GLN D   3 " --> pdb=" O   TYR D  56 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE D   5 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   PHE D  60 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   SER D   7 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   LYS D  88 " --> pdb=" O   GLN D  55 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.267A  pdb=" N   ALA D   4 " --> pdb=" O   TRP D  31 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   GLN D   3 " --> pdb=" O   TYR D  56 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   PHE D   5 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   PHE D  60 " --> pdb=" O   PHE D   5 " (cutoff:3.500A)
      removed outlier: 7.282A  pdb=" N   SER D   7 " --> pdb=" O   PHE D  60 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE D  92 " --> pdb=" O   PHE D  57 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ALA D  59 " --> pdb=" O   ILE D  92 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 148 through 149
      removed outlier: 3.570A  pdb=" N   LEU D 162 " --> pdb=" O   ILE D 155 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG D 153 " --> pdb=" O   VAL D 164 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 148 through 149
      removed outlier: 3.853A  pdb=" N   TYR D 209 " --> pdb=" O   VAL D 165 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE D 167 " --> pdb=" O   TYR D 209 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN D 234 " --> pdb=" O   GLU D 239 " (cutoff:3.500A)

    284 hydrogen bonds defined for protein.
    756 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2599
        1.34 -     1.46: 1565
        1.46 -     1.58: 4458
        1.58 -     1.70: 23
        1.70 -     1.82: 33
  Bond restraints: 8678
  Sorted by residual:
  bond pdb=" CG  PRO C  91 "
       pdb=" CD  PRO C  91 "
    ideal  model  delta    sigma   weight residual
    1.503  1.357  0.146 3.40e-02 8.65e+02 1.84e+01
  bond pdb=" CB  PRO C  91 "
       pdb=" CG  PRO C  91 "
    ideal  model  delta    sigma   weight residual
    1.492  1.697 -0.205 5.00e-02 4.00e+02 1.69e+01
  bond pdb=" N   PRO C  91 "
       pdb=" CD  PRO C  91 "
    ideal  model  delta    sigma   weight residual
    1.473  1.513 -0.040 1.40e-02 5.10e+03 8.35e+00
  bond pdb=" N   ILE B  37 "
       pdb=" CA  ILE B  37 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.23e-02 6.61e+03 6.87e+00
  bond pdb=" N   ILE B  32 "
       pdb=" CA  ILE B  32 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.25e-02 6.40e+03 6.59e+00
  ... (remaining 8673 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.34: 11725
        3.34 -     6.68: 84
        6.68 -    10.02: 17
       10.02 -    13.36: 2
       13.36 -    16.70: 2
  Bond angle restraints: 11830
  Sorted by residual:
  angle pdb=" CA  PRO C  91 "
        pdb=" N   PRO C  91 "
        pdb=" CD  PRO C  91 "
      ideal   model   delta    sigma   weight residual
     112.00   95.30   16.70 1.40e+00 5.10e-01 1.42e+02
  angle pdb=" CA  PRO B 127 "
        pdb=" N   PRO B 127 "
        pdb=" CD  PRO B 127 "
      ideal   model   delta    sigma   weight residual
     112.00  101.99   10.01 1.40e+00 5.10e-01 5.11e+01
  angle pdb=" N   PRO C  91 "
        pdb=" CD  PRO C  91 "
        pdb=" CG  PRO C  91 "
      ideal   model   delta    sigma   weight residual
     103.20   93.05   10.15 1.50e+00 4.44e-01 4.58e+01
  angle pdb=" N   PRO C  91 "
        pdb=" CA  PRO C  91 "
        pdb=" CB  PRO C  91 "
      ideal   model   delta    sigma   weight residual
     103.25   98.78    4.47 1.05e+00 9.07e-01 1.81e+01
  angle pdb=" CA  GLN C  83 "
        pdb=" CB  GLN C  83 "
        pdb=" CG  GLN C  83 "
      ideal   model   delta    sigma   weight residual
     114.10  122.31   -8.21 2.00e+00 2.50e-01 1.68e+01
  ... (remaining 11825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.73: 4429
       20.73 -    41.45: 626
       41.45 -    62.18: 113
       62.18 -    82.90: 30
       82.90 -   103.63: 2
  Dihedral angle restraints: 5200
    sinusoidal: 2230
      harmonic: 2970
  Sorted by residual:
  dihedral pdb=" O1A AR6 B 301 "
           pdb=" O3A AR6 B 301 "
           pdb=" PA  AR6 B 301 "
           pdb=" PB  AR6 B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     277.49  173.86  103.63     1      3.00e+01 1.11e-03 1.32e+01
  dihedral pdb=" CA  ASP D  69 "
           pdb=" CB  ASP D  69 "
           pdb=" CG  ASP D  69 "
           pdb=" OD1 ASP D  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.96   59.96     1      2.00e+01 2.50e-03 1.20e+01
  dihedral pdb=" CA  TRP C  70 "
           pdb=" C   TRP C  70 "
           pdb=" N   CYS C  71 "
           pdb=" CA  CYS C  71 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.93   17.07     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 5197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1058
       0.055 -    0.110: 224
       0.110 -    0.165: 32
       0.165 -    0.220: 3
       0.220 -    0.275: 3
  Chirality restraints: 1320
  Sorted by residual:
  chirality pdb=" CA  PRO C  91 "
            pdb=" N   PRO C  91 "
            pdb=" C   PRO C  91 "
            pdb=" CB  PRO C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C2D AR6 B 301 "
            pdb=" C1D AR6 B 301 "
            pdb=" C3D AR6 B 301 "
            pdb=" O2D AR6 B 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70   -2.43   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" C2D AR6 D 301 "
            pdb=" C1D AR6 D 301 "
            pdb=" C3D AR6 D 301 "
            pdb=" O2D AR6 D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70   -2.44   -0.25 2.00e-01 2.50e+01 1.59e+00
  ... (remaining 1317 not shown)

  Planarity restraints: 1458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 126 "   -0.107 5.00e-02 4.00e+02   1.55e-01 3.82e+01
        pdb=" N   PRO B 127 "    0.267 5.00e-02 4.00e+02
        pdb=" CA  PRO B 127 "   -0.082 5.00e-02 4.00e+02
        pdb=" CD  PRO B 127 "   -0.078 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 126 "   -0.053 5.00e-02 4.00e+02   8.03e-02 1.03e+01
        pdb=" N   PRO D 127 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO D 127 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO D 127 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  90 "   -0.053 5.00e-02 4.00e+02   7.14e-02 8.15e+00
        pdb=" N   PRO C  91 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO C  91 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  91 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1455 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 201
        2.66 -     3.22: 8116
        3.22 -     3.78: 13511
        3.78 -     4.34: 17445
        4.34 -     4.90: 27776
  Nonbonded interactions: 67049
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 237 "
            pdb=" OE1 GLU B 239 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OH  TYR C  56 "
            pdb=" OE1 GLU C 145 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OG  SER A  62 "
            pdb=" OE1 GLU A  64 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   GLU A 114 "
            pdb=" OG1 THR A 118 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER D 245 "
            pdb=" O   LEU D 250 "
     model   vdw
     2.199 3.040
  ... (remaining 67044 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 2 through 33 or resid 42 through 258))
  selection = chain 'C'
  selection = (chain 'D' and (resid 2 through 33 or resid 42 through 258))
}
ncs_group {
  reference = chain 'a'
  selection = chain 'b'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.080
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.040
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.010
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
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      :  0.005   0.205   8678  Z= 0.214
  Angle     :  0.806  16.699  11830  Z= 0.430
  Chirality :  0.048   0.275   1320
  Planarity :  0.007   0.155   1458
  Dihedral  : 18.797 103.628   3268
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  4.90 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 34.30 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.28), residues: 1000
  helix:  0.74 (0.33), residues: 290
  sheet: -0.51 (0.38), residues: 206
  loop : -0.04 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 148 
 TYR   0.024   0.002   TYR C  56 
 PHE   0.012   0.001   PHE A 112 
 TRP   0.049   0.002   TRP A  70 
 HIS   0.003   0.001   HIS B 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 8678)
  covalent geometry    : angle       0.80647 (11830)
  hydrogen bonds       : bond        0.22300 (  282)
  hydrogen bonds       : angle       7.07985 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8484 (tppt) cc_final: 0.7496 (tppt)
REVERT: A  221 THR cc_start: 0.9298 (m) cc_final: 0.8969 (t)
REVERT: B   46 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7930 (mm-40)
REVERT: C  132 ARG cc_start: 0.8966 (ttm-80) cc_final: 0.8739 (ttp-110)
REVERT: D   72 TRP cc_start: 0.8553 (OUTLIER) cc_final: 0.7374 (m-90)
  outliers start: 9
  outliers final: 4
  residues processed: 149
  average time/residue: 0.1192
  time to fit residues: 23.4569
Evaluate side-chains
  123 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   46 GLN
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 ASN
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.096448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.071236 restraints weight = 19210.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.073818 restraints weight = 9774.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.075463 restraints weight = 6294.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.076476 restraints weight = 4737.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.076834 restraints weight = 3985.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   8678  Z= 0.214
  Angle     :  0.670   6.566  11830  Z= 0.343
  Chirality :  0.046   0.225   1320
  Planarity :  0.006   0.092   1458
  Dihedral  : 11.771  95.749   1283
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.80 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 28.06 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.27), residues: 1000
  helix:  0.66 (0.32), residues: 296
  sheet: -0.78 (0.35), residues: 240
  loop : -0.14 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 148 
 TYR   0.021   0.002   TYR B 244 
 PHE   0.012   0.001   PHE B 231 
 TRP   0.026   0.002   TRP A  70 
 HIS   0.003   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 8678)
  covalent geometry    : angle       0.67035 (11830)
  hydrogen bonds       : bond        0.04006 (  282)
  hydrogen bonds       : angle       5.49172 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 124
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9069 (t)
REVERT: B   56 TYR cc_start: 0.7993 (m-10) cc_final: 0.7565 (m-10)
REVERT: C   27 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: C   55 GLN cc_start: 0.5141 (pp30) cc_final: 0.4614 (pp30)
REVERT: C   79 TYR cc_start: 0.8052 (t80) cc_final: 0.7762 (t80)
REVERT: C   83 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8396 (mm-40)
REVERT: C   99 GLN cc_start: 0.8216 (pm20) cc_final: 0.7773 (pm20)
REVERT: D   72 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.7235 (m-90)
REVERT: D  107 ASP cc_start: 0.8659 (p0) cc_final: 0.8442 (p0)
  outliers start: 39
  outliers final: 22
  residues processed: 153
  average time/residue: 0.1067
  time to fit residues: 22.0418
Evaluate side-chains
  137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Chi-restraints excluded: chain D residue  182 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 75 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 28 optimal weight:    0.3980
   chunk 83 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A   8 HIS
C  83 GLN
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.100474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.075389 restraints weight = 18806.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.078168 restraints weight = 9380.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.079884 restraints weight = 5890.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.080858 restraints weight = 4396.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.081559 restraints weight = 3697.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8678  Z= 0.110
  Angle     :  0.592   8.608  11830  Z= 0.300
  Chirality :  0.044   0.219   1320
  Planarity :  0.005   0.083   1458
  Dihedral  : 11.344  98.371   1278
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.30 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 27.73 %
    Favored  : 68.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.28), residues: 1000
  helix:  0.79 (0.32), residues: 294
  sheet: -0.73 (0.35), residues: 240
  loop : -0.06 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 132 
 TYR   0.016   0.001   TYR C 209 
 PHE   0.010   0.001   PHE A   5 
 TRP   0.025   0.001   TRP A  70 
 HIS   0.003   0.001   HIS A   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8678)
  covalent geometry    : angle       0.59196 (11830)
  hydrogen bonds       : bond        0.03222 (  282)
  hydrogen bonds       : angle       5.03948 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7246 (p-90) cc_final: 0.6471 (p-90)
REVERT: A  132 ARG cc_start: 0.8617 (tmt170) cc_final: 0.8260 (mmm160)
REVERT: A  188 ASP cc_start: 0.8934 (p0) cc_final: 0.8422 (p0)
REVERT: A  221 THR cc_start: 0.9344 (m) cc_final: 0.9141 (t)
REVERT: B   70 TRP cc_start: 0.7807 (m-10) cc_final: 0.7583 (m-10)
REVERT: C   55 GLN cc_start: 0.4811 (pp30) cc_final: 0.4551 (pp30)
REVERT: C   83 GLN cc_start: 0.8745 (mm110) cc_final: 0.8509 (mm-40)
REVERT: C   99 GLN cc_start: 0.8228 (pm20) cc_final: 0.8018 (pm20)
REVERT: D   72 TRP cc_start: 0.8726 (OUTLIER) cc_final: 0.7375 (m-90)
REVERT: D  187 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8449 (mt-10)
  outliers start: 34
  outliers final: 18
  residues processed: 156
  average time/residue: 0.1058
  time to fit residues: 22.1031
Evaluate side-chains
  134 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 92 optimal weight:    0.0050
   chunk 18 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.1196

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.100416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.075053 restraints weight = 19204.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.077814 restraints weight = 9615.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079559 restraints weight = 6099.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.080631 restraints weight = 4537.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.081237 restraints weight = 3790.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.1947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8678  Z= 0.113
  Angle     :  0.568   6.887  11830  Z= 0.287
  Chirality :  0.044   0.219   1320
  Planarity :  0.005   0.070   1458
  Dihedral  : 11.134 105.946   1278
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.90 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.62 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.27), residues: 1000
  helix:  0.98 (0.32), residues: 286
  sheet: -0.74 (0.35), residues: 240
  loop : -0.10 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 132 
 TYR   0.016   0.001   TYR C 209 
 PHE   0.010   0.001   PHE A   5 
 TRP   0.016   0.001   TRP A  70 
 HIS   0.003   0.001   HIS D  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8678)
  covalent geometry    : angle       0.56831 (11830)
  hydrogen bonds       : bond        0.03009 (  282)
  hydrogen bonds       : angle       4.85001 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 120
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 TRP cc_start: 0.7201 (p-90) cc_final: 0.6470 (p-90)
REVERT: A  132 ARG cc_start: 0.8627 (tmt170) cc_final: 0.8282 (mmm160)
REVERT: A  188 ASP cc_start: 0.8933 (p0) cc_final: 0.8485 (p0)
REVERT: C   27 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8615 (mm)
REVERT: C   77 GLN cc_start: 0.9189 (mt0) cc_final: 0.8872 (mm-40)
REVERT: C   99 GLN cc_start: 0.8367 (pm20) cc_final: 0.8149 (pm20)
REVERT: D   72 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.7089 (m-90)
REVERT: D  187 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8461 (mt-10)
  outliers start: 38
  outliers final: 24
  residues processed: 149
  average time/residue: 0.1031
  time to fit residues: 20.6302
Evaluate side-chains
  139 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 ILE
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   chunk 59 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 85 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 144 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.095657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.070129 restraints weight = 19265.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.072719 restraints weight = 9872.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.074397 restraints weight = 6393.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.075393 restraints weight = 4803.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.075888 restraints weight = 4047.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8678  Z= 0.212
  Angle     :  0.642   8.510  11830  Z= 0.324
  Chirality :  0.046   0.276   1320
  Planarity :  0.005   0.090   1458
  Dihedral  : 11.081 110.254   1278
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.80 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 28.29 %
    Favored  : 67.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.28), residues: 1000
  helix:  0.98 (0.33), residues: 286
  sheet: -0.76 (0.36), residues: 240
  loop : -0.23 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 148 
 TYR   0.016   0.002   TYR B 244 
 PHE   0.014   0.001   PHE A 112 
 TRP   0.016   0.002   TRP B  70 
 HIS   0.004   0.001   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 8678)
  covalent geometry    : angle       0.64204 (11830)
  hydrogen bonds       : bond        0.03329 (  282)
  hydrogen bonds       : angle       4.86011 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 116
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8845 (m-30) cc_final: 0.8204 (p0)
REVERT: A  132 ARG cc_start: 0.8631 (tmt170) cc_final: 0.8266 (mmm160)
REVERT: A  188 ASP cc_start: 0.8990 (p0) cc_final: 0.8627 (p0)
REVERT: B  229 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8691 (t)
REVERT: C    6 PHE cc_start: 0.8396 (m-10) cc_final: 0.8099 (m-10)
REVERT: C   27 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8736 (mm)
REVERT: C   77 GLN cc_start: 0.9267 (mt0) cc_final: 0.8951 (mm-40)
REVERT: C   83 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8464 (mm-40)
REVERT: C   99 GLN cc_start: 0.8423 (pm20) cc_final: 0.8190 (pm20)
REVERT: C  145 GLU cc_start: 0.8871 (tp30) cc_final: 0.8426 (tp30)
REVERT: D   72 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.7627 (m-90)
REVERT: D  187 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8492 (mt-10)
  outliers start: 42
  outliers final: 29
  residues processed: 149
  average time/residue: 0.1000
  time to fit residues: 20.3555
Evaluate side-chains
  141 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  229 THR
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 95 optimal weight:    0.4980
   chunk 44 optimal weight:    5.9990
   chunk 78 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 144 ASN
** C   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.096191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.070732 restraints weight = 19206.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.073334 restraints weight = 9750.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.075042 restraints weight = 6278.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.076053 restraints weight = 4689.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.076693 restraints weight = 3934.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8678  Z= 0.170
  Angle     :  0.616   8.408  11830  Z= 0.311
  Chirality :  0.045   0.258   1320
  Planarity :  0.005   0.072   1458
  Dihedral  : 11.074 110.033   1278
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.40 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 30.62 %
    Favored  : 65.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.28), residues: 1000
  helix:  0.94 (0.32), residues: 286
  sheet: -0.76 (0.36), residues: 240
  loop : -0.25 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 132 
 TYR   0.017   0.002   TYR C  56 
 PHE   0.011   0.001   PHE A 112 
 TRP   0.014   0.001   TRP B  70 
 HIS   0.003   0.001   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 8678)
  covalent geometry    : angle       0.61647 (11830)
  hydrogen bonds       : bond        0.03131 (  282)
  hydrogen bonds       : angle       4.78698 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 114
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8808 (m-30) cc_final: 0.8164 (p0)
REVERT: A  132 ARG cc_start: 0.8628 (tmt170) cc_final: 0.8266 (mmm160)
REVERT: A  188 ASP cc_start: 0.8977 (p0) cc_final: 0.8633 (p0)
REVERT: B   72 TRP cc_start: 0.8469 (OUTLIER) cc_final: 0.8203 (t60)
REVERT: C    6 PHE cc_start: 0.8374 (m-10) cc_final: 0.8132 (m-10)
REVERT: C   27 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8740 (mm)
REVERT: C   77 GLN cc_start: 0.9244 (mt0) cc_final: 0.8931 (mm-40)
REVERT: C   99 GLN cc_start: 0.8446 (pm20) cc_final: 0.8201 (pm20)
REVERT: C  145 GLU cc_start: 0.8806 (tp30) cc_final: 0.8315 (tp30)
REVERT: D   72 TRP cc_start: 0.8881 (OUTLIER) cc_final: 0.7429 (m-90)
  outliers start: 34
  outliers final: 26
  residues processed: 139
  average time/residue: 0.0965
  time to fit residues: 18.1487
Evaluate side-chains
  137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0050
   chunk 23 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    2.0000

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 163 GLN
** D   8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.096749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.071486 restraints weight = 19311.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.074154 restraints weight = 9733.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.075790 restraints weight = 6188.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.076923 restraints weight = 4645.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.077473 restraints weight = 3855.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8569
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8678  Z= 0.149
  Angle     :  0.609   8.445  11830  Z= 0.308
  Chirality :  0.044   0.254   1320
  Planarity :  0.005   0.069   1458
  Dihedral  : 11.041 110.142   1278
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.30 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 31.29 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.28), residues: 1000
  helix:  0.90 (0.32), residues: 286
  sheet: -0.75 (0.36), residues: 240
  loop : -0.23 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 132 
 TYR   0.021   0.001   TYR C  56 
 PHE   0.010   0.001   PHE A 112 
 TRP   0.015   0.001   TRP A  31 
 HIS   0.003   0.001   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8678)
  covalent geometry    : angle       0.60909 (11830)
  hydrogen bonds       : bond        0.03013 (  282)
  hydrogen bonds       : angle       4.74681 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 TRP cc_start: 0.8415 (m-10) cc_final: 0.8016 (m-10)
REVERT: A   73 ASP cc_start: 0.8772 (m-30) cc_final: 0.8167 (p0)
REVERT: A  132 ARG cc_start: 0.8638 (tmt170) cc_final: 0.8275 (mmm160)
REVERT: A  188 ASP cc_start: 0.8940 (p0) cc_final: 0.8621 (p0)
REVERT: A  221 THR cc_start: 0.9297 (t) cc_final: 0.9086 (t)
REVERT: B   72 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.8163 (t60)
REVERT: C   27 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8726 (mm)
REVERT: C   77 GLN cc_start: 0.9252 (mt0) cc_final: 0.8952 (mm-40)
REVERT: C   83 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8397 (mm-40)
REVERT: C   99 GLN cc_start: 0.8435 (pm20) cc_final: 0.8178 (pm20)
REVERT: C  145 GLU cc_start: 0.8813 (tp30) cc_final: 0.8232 (tp30)
REVERT: D   72 TRP cc_start: 0.8872 (OUTLIER) cc_final: 0.7306 (m-90)
  outliers start: 36
  outliers final: 27
  residues processed: 149
  average time/residue: 0.1044
  time to fit residues: 20.8064
Evaluate side-chains
  148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue   72 TRP
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.093985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.068760 restraints weight = 18993.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.071317 restraints weight = 9656.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.072995 restraints weight = 6184.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.074038 restraints weight = 4616.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.074622 restraints weight = 3828.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8678  Z= 0.182
  Angle     :  0.642   8.429  11830  Z= 0.325
  Chirality :  0.045   0.271   1320
  Planarity :  0.005   0.072   1458
  Dihedral  : 11.041 111.679   1278
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.70 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 31.51 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.28), residues: 1000
  helix:  0.86 (0.32), residues: 286
  sheet: -0.57 (0.37), residues: 234
  loop : -0.31 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 148 
 TYR   0.016   0.002   TYR C 209 
 PHE   0.010   0.001   PHE B 231 
 TRP   0.014   0.001   TRP A  31 
 HIS   0.004   0.001   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 8678)
  covalent geometry    : angle       0.64246 (11830)
  hydrogen bonds       : bond        0.03175 (  282)
  hydrogen bonds       : angle       4.77125 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 123
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.9370 (mp10) cc_final: 0.8595 (mp10)
REVERT: A   31 TRP cc_start: 0.8413 (m-10) cc_final: 0.8030 (m-10)
REVERT: A  110 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7485 (mmt90)
REVERT: A  132 ARG cc_start: 0.8656 (tmt170) cc_final: 0.8309 (mmm160)
REVERT: A  176 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.9015 (t)
REVERT: B   72 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.8181 (t60)
REVERT: C   27 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8744 (mm)
REVERT: C   77 GLN cc_start: 0.9236 (mt0) cc_final: 0.8943 (mm-40)
REVERT: C   83 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8350 (mm-40)
REVERT: C   99 GLN cc_start: 0.8436 (pm20) cc_final: 0.8028 (pm20)
REVERT: C  145 GLU cc_start: 0.8817 (tp30) cc_final: 0.8423 (tp30)
REVERT: D  188 ASP cc_start: 0.8634 (m-30) cc_final: 0.8248 (t0)
  outliers start: 34
  outliers final: 27
  residues processed: 150
  average time/residue: 0.0902
  time to fit residues: 18.6223
Evaluate side-chains
  148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 118
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   32 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0770
   chunk 34 optimal weight:    0.0170
   overall best weight:    0.9578

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.097993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.073426 restraints weight = 18665.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.076101 restraints weight = 9261.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.077828 restraints weight = 5814.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.078791 restraints weight = 4295.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.079486 restraints weight = 3585.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8678  Z= 0.118
  Angle     :  0.621   9.286  11830  Z= 0.314
  Chirality :  0.045   0.242   1320
  Planarity :  0.005   0.073   1458
  Dihedral  : 10.929 110.370   1276
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.20 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 32.52 %
    Favored  : 64.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.28), residues: 1000
  helix:  0.91 (0.33), residues: 286
  sheet: -0.66 (0.36), residues: 238
  loop : -0.26 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 132 
 TYR   0.016   0.001   TYR C 209 
 PHE   0.010   0.001   PHE A 112 
 TRP   0.027   0.001   TRP C  72 
 HIS   0.002   0.000   HIS D   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8678)
  covalent geometry    : angle       0.62122 (11830)
  hydrogen bonds       : bond        0.02961 (  282)
  hydrogen bonds       : angle       4.72221 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 130
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.9278 (mp10) cc_final: 0.8599 (mt0)
REVERT: A   73 ASP cc_start: 0.8706 (m-30) cc_final: 0.8109 (p0)
REVERT: A  110 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7493 (mmt90)
REVERT: A  132 ARG cc_start: 0.8609 (tmt170) cc_final: 0.8262 (mmm160)
REVERT: A  188 ASP cc_start: 0.8926 (p0) cc_final: 0.8581 (p0)
REVERT: B   72 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.8170 (t60)
REVERT: C   27 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8667 (mm)
REVERT: C   77 GLN cc_start: 0.9138 (mt0) cc_final: 0.8891 (mm-40)
REVERT: C   99 GLN cc_start: 0.8474 (pm20) cc_final: 0.8061 (pm20)
REVERT: C  145 GLU cc_start: 0.8719 (tp30) cc_final: 0.8441 (tp30)
REVERT: D   20 LEU cc_start: 0.9304 (tt) cc_final: 0.9077 (tt)
REVERT: D  101 ASP cc_start: 0.8255 (t0) cc_final: 0.7985 (t0)
REVERT: D  177 ASP cc_start: 0.8833 (p0) cc_final: 0.8510 (p0)
REVERT: D  188 ASP cc_start: 0.8537 (m-30) cc_final: 0.8163 (t0)
  outliers start: 29
  outliers final: 24
  residues processed: 150
  average time/residue: 0.1050
  time to fit residues: 21.1193
Evaluate side-chains
  147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 9 optimal weight:   30.0000
   chunk 50 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0670
   chunk 73 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 92 optimal weight:    0.0570
   overall best weight:    3.0242

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

Flipped N/Q/H residues before XYZ refinement:
B  46 GLN
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.093375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.068626 restraints weight = 18733.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.071172 restraints weight = 9526.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.072847 restraints weight = 6064.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.073858 restraints weight = 4486.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.074416 restraints weight = 3729.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8678  Z= 0.202
  Angle     :  0.666   8.967  11830  Z= 0.340
  Chirality :  0.046   0.266   1320
  Planarity :  0.005   0.075   1458
  Dihedral  : 10.968 112.577   1274
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.60 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 32.52 %
    Favored  : 64.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.28), residues: 1000
  helix:  0.88 (0.32), residues: 286
  sheet: -0.63 (0.37), residues: 238
  loop : -0.32 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 132 
 TYR   0.015   0.002   TYR B 244 
 PHE   0.011   0.001   PHE D 231 
 TRP   0.020   0.002   TRP C  72 
 HIS   0.004   0.001   HIS B  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 8678)
  covalent geometry    : angle       0.66590 (11830)
  hydrogen bonds       : bond        0.03288 (  282)
  hydrogen bonds       : angle       4.85267 (  756)

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

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

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2000 Ramachandran restraints generated.
    1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 GLN cc_start: 0.9310 (mp10) cc_final: 0.8627 (mt0)
REVERT: A   73 ASP cc_start: 0.8784 (m-30) cc_final: 0.8155 (p0)
REVERT: A  110 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7445 (mmt90)
REVERT: A  132 ARG cc_start: 0.8656 (tmt170) cc_final: 0.8310 (mmm160)
REVERT: A  176 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9043 (t)
REVERT: A  188 ASP cc_start: 0.8992 (p0) cc_final: 0.8536 (p0)
REVERT: B   72 TRP cc_start: 0.8617 (OUTLIER) cc_final: 0.8220 (t60)
REVERT: B  209 TYR cc_start: 0.8916 (t80) cc_final: 0.8147 (t80)
REVERT: C   27 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8733 (mm)
REVERT: C   77 GLN cc_start: 0.9149 (mt0) cc_final: 0.8893 (mm-40)
REVERT: C   83 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8360 (mm-40)
REVERT: C   99 GLN cc_start: 0.8486 (pm20) cc_final: 0.8047 (pm20)
REVERT: D  188 ASP cc_start: 0.8550 (m-30) cc_final: 0.8210 (t0)
  outliers start: 31
  outliers final: 25
  residues processed: 138
  average time/residue: 0.1049
  time to fit residues: 19.6051
Evaluate side-chains
  137 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  206 VAL
Chi-restraints excluded: chain A residue  217 TYR
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain B residue   12 ASP
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue  102 LEU
Chi-restraints excluded: chain C residue  103 ASN
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  147 VAL
Chi-restraints excluded: chain C residue  193 SER
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  232 VAL
Chi-restraints excluded: chain D residue   67 LYS
Chi-restraints excluded: chain D residue  106 THR
Chi-restraints excluded: chain D residue  164 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0970
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** B  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.099290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.073834 restraints weight = 18911.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.076565 restraints weight = 9580.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.078316 restraints weight = 6101.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.079395 restraints weight = 4545.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.080033 restraints weight = 3795.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8514
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8678  Z= 0.114
  Angle     :  0.626   9.396  11830  Z= 0.316
  Chirality :  0.044   0.241   1320
  Planarity :  0.005   0.075   1458
  Dihedral  : 10.897 110.552   1274
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.50 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 33.41 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.28), residues: 1000
  helix:  0.87 (0.32), residues: 286
  sheet: -0.79 (0.37), residues: 234
  loop : -0.23 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 110 
 TYR   0.017   0.001   TYR C  56 
 PHE   0.009   0.001   PHE A 112 
 TRP   0.013   0.001   TRP D  72 
 HIS   0.002   0.000   HIS D   8 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8678)
  covalent geometry    : angle       0.62557 (11830)
  hydrogen bonds       : bond        0.02933 (  282)
  hydrogen bonds       : angle       4.73904 (  756)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.27 seconds
wall clock time: 26 minutes 36.01 seconds (1596.01 seconds total)