Starting phenix.real_space_refine
on Tue Feb  3 20:27:35 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zk1_60163/02_2026/8zk1_60163.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zk1_60163/02_2026/8zk1_60163.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zk1_60163/02_2026/8zk1_60163.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zk1_60163/02_2026/8zk1_60163.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zk1_60163/02_2026/8zk1_60163.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zk1_60163/02_2026/8zk1_60163.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    4174      2.51       5
     N    1146      2.21       5
     O    1261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6619
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1691
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 202}
    Chain: "B"
      Number of atoms: 1691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1691
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202}
    Chain: "E"
      Number of atoms: 1619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1619
          Classifications: {'peptide': 214}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 202}
    Chain: "F"
      Number of atoms: 1618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1618
          Classifications: {'peptide': 214}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 203}
  Time building chain proxies: 1.56, per 1000 atoms: 0.24
  Number of scatterers: 6619
  At special positions: 0
  Unit cell: (119.57, 107.613, 128.266, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1261      8.00
     N    1146      7.00
     C    4174      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  51 " - pdb=" SG  CYS B 125 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 165 " - pdb=" SG  CYS B 219 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  52 " - pdb=" SG  CYS E 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 166 " - pdb=" SG  CYS E 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  52 " - pdb=" SG  CYS F 126 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 166 " - pdb=" SG  CYS F 220 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 315.4 milliseconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1558

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 18 sheets defined
      2.7% alpha, 42.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 116 through 120
      removed outlier: 3.870A  pdb=" N   ASN A 120 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.954A  pdb=" N   PHE A 240 " --> pdb=" O   PRO A 237 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   MET A 241 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 237 through 241'
    Processing helix  chain 'E' and resid 103 through 106
    Processing helix  chain 'F' and resid 90 through 94
    Processing helix  chain 'F' and resid 239 through 242
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41
      removed outlier: 3.712A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   VAL A  77 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 151
      removed outlier: 3.593A  pdb=" N   LEU A 150 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 5.892A  pdb=" N   PHE A 201 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157
    Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 179
    Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 33
      removed outlier: 3.649A  pdb=" N   ALA B 109 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 83
      removed outlier: 3.745A  pdb=" N   ARG B  82 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   LYS B  79 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 83
      removed outlier: 3.745A  pdb=" N   ARG B  82 " --> pdb=" O   LYS B  79 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   LYS B  79 " --> pdb=" O   ARG B  82 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 153
      removed outlier: 5.532A  pdb=" N   ARG B 162 " --> pdb=" O   ILE B 209 " (cutoff:3.500A)
      removed outlier: 7.026A  pdb=" N   ILE B 209 " --> pdb=" O   ARG B 162 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   GLU B 164 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   VAL B 207 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   ILE B 166 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   THR B 205 " --> pdb=" O   ILE B 166 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   ARG B 168 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL B 203 " --> pdb=" O   ARG B 168 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   LYS B 190 " --> pdb=" O   ALA B 206 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 186
      removed outlier: 4.762A  pdb=" N   TRP B 178 " --> pdb=" O   ALA B 186 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 185 through 186
      removed outlier: 4.762A  pdb=" N   TRP B 178 " --> pdb=" O   ALA B 186 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 33 through 34
      removed outlier: 3.649A  pdb=" N   HIS E  53 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 40 through 43
      removed outlier: 6.285A  pdb=" N   ILE E  40 " --> pdb=" O   LYS E 142 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   ALA E 144 " --> pdb=" O   ILE E  40 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ALA E  42 " --> pdb=" O   ALA E 144 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU E  65 " --> pdb=" O   VAL E  78 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   VAL E  78 " --> pdb=" O   LEU E  65 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   TRP E  67 " --> pdb=" O   VAL E  76 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 190 through 191
      removed outlier: 6.611A  pdb=" N   VAL E 204 " --> pdb=" O   THR E 169 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   THR E 169 " --> pdb=" O   VAL E 204 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ALA E 206 " --> pdb=" O   ARG E 167 " (cutoff:3.500A)
      removed outlier: 5.269A  pdb=" N   ARG E 167 " --> pdb=" O   ALA E 206 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   VAL E 208 " --> pdb=" O   GLU E 165 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   GLU E 165 " --> pdb=" O   VAL E 208 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   MET E 210 " --> pdb=" O   HIS E 163 " (cutoff:3.500A)
      removed outlier: 5.511A  pdb=" N   HIS E 163 " --> pdb=" O   MET E 210 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   HIS E 163 " --> pdb=" O   LYS E 155 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   SER F 236 " --> pdb=" O   VAL E 152 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 176 through 177
    Processing sheet with id=AB7, first strand: chain 'E' and resid 176 through 177
      removed outlier: 9.240A  pdb=" N   VAL F 152 " --> pdb=" O   THR E 232 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   SER E 234 " --> pdb=" O   VAL F 152 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   HIS F 163 " --> pdb=" O   MET F 210 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   MET F 210 " --> pdb=" O   HIS F 163 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   GLU F 165 " --> pdb=" O   VAL F 208 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   VAL F 208 " --> pdb=" O   GLU F 165 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   ARG F 167 " --> pdb=" O   ALA F 206 " (cutoff:3.500A)
      removed outlier: 7.405A  pdb=" N   ALA F 206 " --> pdb=" O   ARG F 167 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   THR F 169 " --> pdb=" O   VAL F 204 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   VAL F 204 " --> pdb=" O   THR F 169 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER F 207 " --> pdb=" O   VAL F 190 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL F 190 " --> pdb=" O   SER F 207 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 34
      removed outlier: 3.520A  pdb=" N   GLY F 103 " --> pdb=" O   LYS F 108 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ALA F 110 " --> pdb=" O   ARG F 101 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   ARG F 101 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   ARG F 112 " --> pdb=" O   ILE F  99 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   ILE F  99 " --> pdb=" O   ARG F 112 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 43
      removed outlier: 6.034A  pdb=" N   ILE F  40 " --> pdb=" O   LYS F 142 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   ALA F 144 " --> pdb=" O   ILE F  40 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA F  42 " --> pdb=" O   ALA F 144 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU F  65 " --> pdb=" O   VAL F  78 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   VAL F  78 " --> pdb=" O   LEU F  65 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   TRP F  67 " --> pdb=" O   VAL F  76 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    555 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: 0.98

  Time building geometry restraints manager: 0.81 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: 2203
        1.34 -     1.46: 1518
        1.46 -     1.58: 2978
        1.58 -     1.70: 0
        1.70 -     1.82: 60
  Bond restraints: 6759
  Sorted by residual:
  bond pdb=" N   PRO B  55 "
       pdb=" CA  PRO B  55 "
    ideal  model  delta    sigma   weight residual
    1.469  1.482 -0.014 1.28e-02 6.10e+03 1.11e+00
  bond pdb=" C   ASP F 239 "
       pdb=" N   PRO F 240 "
    ideal  model  delta    sigma   weight residual
    1.336  1.347 -0.011 1.08e-02 8.57e+03 1.06e+00
  bond pdb=" C   SER A  72 "
       pdb=" O   SER A  72 "
    ideal  model  delta    sigma   weight residual
    1.248  1.238  0.011 1.26e-02 6.30e+03 7.60e-01
  bond pdb=" CB  PRO E 193 "
       pdb=" CG  PRO E 193 "
    ideal  model  delta    sigma   weight residual
    1.492  1.535 -0.043 5.00e-02 4.00e+02 7.49e-01
  bond pdb=" CA  VAL A 185 "
       pdb=" CB  VAL A 185 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.05e-02 9.07e+03 7.44e-01
  ... (remaining 6754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 8962
        1.73 -     3.45: 170
        3.45 -     5.18: 20
        5.18 -     6.91: 1
        6.91 -     8.64: 2
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" C   GLY E 131 "
        pdb=" N   ASP E 132 "
        pdb=" CA  ASP E 132 "
      ideal   model   delta    sigma   weight residual
     121.70  130.34   -8.64 1.80e+00 3.09e-01 2.30e+01
  angle pdb=" N   SER B  69 "
        pdb=" CA  SER B  69 "
        pdb=" C   SER B  69 "
      ideal   model   delta    sigma   weight residual
     114.62  111.58    3.04 1.14e+00 7.69e-01 7.12e+00
  angle pdb=" C   SER B  54 "
        pdb=" N   PRO B  55 "
        pdb=" CA  PRO B  55 "
      ideal   model   delta    sigma   weight residual
     119.84  116.84    3.00 1.25e+00 6.40e-01 5.75e+00
  angle pdb=" CA  SER B  69 "
        pdb=" C   SER B  69 "
        pdb=" N   GLN B  70 "
      ideal   model   delta    sigma   weight residual
     119.71  116.92    2.79 1.17e+00 7.31e-01 5.70e+00
  angle pdb=" N   ARG A  95 "
        pdb=" CA  ARG A  95 "
        pdb=" C   ARG A  95 "
      ideal   model   delta    sigma   weight residual
     114.31  111.31    3.00 1.29e+00 6.01e-01 5.41e+00
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3583
       17.99 -    35.98: 416
       35.98 -    53.97: 54
       53.97 -    71.96: 14
       71.96 -    89.95: 12
  Dihedral angle restraints: 4079
    sinusoidal: 1637
      harmonic: 2442
  Sorted by residual:
  dihedral pdb=" CA  VAL F  78 "
           pdb=" C   VAL F  78 "
           pdb=" N   TYR F  79 "
           pdb=" CA  TYR F  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.29   17.71     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  SER B  72 "
           pdb=" C   SER B  72 "
           pdb=" N   PRO B  73 "
           pdb=" CA  PRO B  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.98   17.02     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  SER B  54 "
           pdb=" C   SER B  54 "
           pdb=" N   PRO B  55 "
           pdb=" CA  PRO B  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.98   17.02     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 4076 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 560
       0.030 -    0.060: 294
       0.060 -    0.090: 67
       0.090 -    0.120: 76
       0.120 -    0.151: 13
  Chirality restraints: 1010
  Sorted by residual:
  chirality pdb=" CA  ILE F 187 "
            pdb=" N   ILE F 187 "
            pdb=" C   ILE F 187 "
            pdb=" CB  ILE F 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.67e-01
  chirality pdb=" CA  ILE E 209 "
            pdb=" N   ILE E 209 "
            pdb=" C   ILE E 209 "
            pdb=" CB  ILE E 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality pdb=" CA  ILE E 222 "
            pdb=" N   ILE E 222 "
            pdb=" C   ILE E 222 "
            pdb=" CB  ILE E 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  ... (remaining 1007 not shown)

  Planarity restraints: 1192
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  54 "   -0.069 5.00e-02 4.00e+02   1.06e-01 1.78e+01
        pdb=" N   PRO B  55 "    0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO B  55 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO B  55 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA E 192 "    0.045 5.00e-02 4.00e+02   6.69e-02 7.17e+00
        pdb=" N   PRO E 193 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO E 193 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E 193 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 241 "    0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B 242 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 242 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 242 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1189 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 69
        2.58 -     3.16: 5395
        3.16 -     3.74: 9193
        3.74 -     4.32: 12640
        4.32 -     4.90: 22054
  Nonbonded interactions: 49351
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 232 "
            pdb=" OD2 ASP F 149 "
     model   vdw
     1.999 3.040
  nonbonded pdb=" N   GLU A 231 "
            pdb=" OE1 GLU A 231 "
     model   vdw
     2.084 3.120
  nonbonded pdb=" N   GLN E 174 "
            pdb=" OE1 GLN E 174 "
     model   vdw
     2.118 3.120
  nonbonded pdb=" N   GLN E 178 "
            pdb=" OE1 GLN E 178 "
     model   vdw
     2.140 3.120
  nonbonded pdb=" N   GLU F  46 "
            pdb=" OE1 GLU F  46 "
     model   vdw
     2.176 3.120
  ... (remaining 49346 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'E' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ 
gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 
2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or  \ 
resid 225 through 243))
  selection = (chain 'F' and (resid 30 through 148 or resid 150 through 152 or resid 154 throu \ 
gh 157 or resid 159 through 181 or resid 183 through 188 or resid 190 through 20 \ 
2 or resid 204 through 212 or resid 214 through 220 or resid 222 through 223 or  \ 
resid 225 through 243))
}

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=0.00 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:             2.880
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.950
  Find NCS groups from input model:        0.120
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
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      :  0.003   0.043   6767  Z= 0.126
  Angle     :  0.604   8.636   9171  Z= 0.334
  Chirality :  0.046   0.151   1010
  Planarity :  0.005   0.106   1192
  Dihedral  : 15.676  89.948   2497
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 19.64 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -2.35 (0.28), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.90 (0.25), residues: 432
  loop : -2.28 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 101 
 TYR   0.013   0.001   TYR E 127 
 PHE   0.010   0.001   PHE F 128 
 TRP   0.019   0.001   TRP F 179 
 HIS   0.005   0.001   HIS F  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6759)
  covalent geometry    : angle       0.60377 ( 9155)
  SS BOND              : bond        0.00445 (    8)
  SS BOND              : angle       0.88144 (   16)
  hydrogen bonds       : bond        0.14464 (  216)
  hydrogen bonds       : angle       7.25442 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 137
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: B  102 ASP cc_start: 0.7370 (t0) cc_final: 0.5859 (t0)
REVERT: E   88 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7164 (ptt180)
  outliers start: 3
  outliers final: 2
  residues processed: 138
  average time/residue: 0.0900
  time to fit residues: 15.9355
Evaluate side-chains
  121 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain E residue   77 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0980
   chunk 74 optimal weight:    0.0000
   overall best weight:    0.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 113 HIS
E  30 GLN
E  89 GLN
E 114 HIS
E 149 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.166570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.158590 restraints weight = 10621.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.158570 restraints weight = 11134.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.159431 restraints weight = 10186.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.159684 restraints weight = 7294.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.160076 restraints weight = 6709.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6767  Z= 0.133
  Angle     :  0.636  10.323   9171  Z= 0.334
  Chirality :  0.047   0.166   1010
  Planarity :  0.005   0.060   1192
  Dihedral  :  5.131  55.795    940
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 19.78 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.85 (0.28), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.57 (0.25), residues: 422
  loop : -1.92 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 168 
 TYR   0.019   0.002   TYR B 126 
 PHE   0.013   0.001   PHE F 128 
 TRP   0.016   0.001   TRP F 179 
 HIS   0.008   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6759)
  covalent geometry    : angle       0.63561 ( 9155)
  SS BOND              : bond        0.00473 (    8)
  SS BOND              : angle       0.64356 (   16)
  hydrogen bonds       : bond        0.03666 (  216)
  hydrogen bonds       : angle       6.30343 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.7829 (mtt) cc_final: 0.7595 (mtt)
REVERT: B  236 ILE cc_start: 0.8383 (tt) cc_final: 0.8054 (mm)
REVERT: F   34 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6660 (mp)
  outliers start: 19
  outliers final: 7
  residues processed: 140
  average time/residue: 0.0873
  time to fit residues: 15.8564
Evaluate side-chains
  121 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain F residue   34 LEU
Chi-restraints excluded: chain F residue   78 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 228 GLN
E 114 HIS
E 149 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.167272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.156930 restraints weight = 10645.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.158337 restraints weight = 7679.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.159207 restraints weight = 5862.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.159946 restraints weight = 4738.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.160314 restraints weight = 3996.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.1795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6767  Z= 0.158
  Angle     :  0.629   8.143   9171  Z= 0.329
  Chirality :  0.047   0.149   1010
  Planarity :  0.004   0.057   1192
  Dihedral  :  5.317  56.158    940
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 22.42 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.71 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.50 (0.25), residues: 430
  loop : -1.81 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 168 
 TYR   0.018   0.002   TYR B 126 
 PHE   0.014   0.002   PHE F 128 
 TRP   0.016   0.001   TRP F 179 
 HIS   0.004   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6759)
  covalent geometry    : angle       0.62774 ( 9155)
  SS BOND              : bond        0.00520 (    8)
  SS BOND              : angle       1.03763 (   16)
  hydrogen bonds       : bond        0.03561 (  216)
  hydrogen bonds       : angle       6.24207 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.7690 (mtt) cc_final: 0.7419 (mtt)
REVERT: F  101 ARG cc_start: 0.6853 (mtm-85) cc_final: 0.6398 (mtp-110)
  outliers start: 30
  outliers final: 17
  residues processed: 141
  average time/residue: 0.0794
  time to fit residues: 14.7987
Evaluate side-chains
  128 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   63 MET
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 52 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 83 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 76 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
E 114 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.164971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.157664 restraints weight = 10563.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.157276 restraints weight = 10667.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.157826 restraints weight = 9717.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.158288 restraints weight = 8253.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.158400 restraints weight = 7721.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6767  Z= 0.171
  Angle     :  0.647   7.742   9171  Z= 0.337
  Chirality :  0.047   0.150   1010
  Planarity :  0.005   0.059   1192
  Dihedral  :  5.414  55.119    940
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 23.68 %
    Favored  : 72.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.65 (0.28), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.41 (0.25), residues: 427
  loop : -1.83 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 101 
 TYR   0.019   0.002   TYR A  78 
 PHE   0.014   0.002   PHE F 128 
 TRP   0.017   0.001   TRP F 179 
 HIS   0.003   0.001   HIS E 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 6759)
  covalent geometry    : angle       0.64564 ( 9155)
  SS BOND              : bond        0.00492 (    8)
  SS BOND              : angle       1.10339 (   16)
  hydrogen bonds       : bond        0.03552 (  216)
  hydrogen bonds       : angle       6.24814 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.7799 (mtt) cc_final: 0.7577 (mtt)
REVERT: F  101 ARG cc_start: 0.6587 (mtm-85) cc_final: 0.6204 (mtp-110)
REVERT: F  232 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9203 (t)
  outliers start: 30
  outliers final: 20
  residues processed: 139
  average time/residue: 0.0784
  time to fit residues: 14.1397
Evaluate side-chains
  135 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  113 HIS
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   63 MET
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   63 MET
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  139 VAL
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0040
   chunk 20 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
F  53 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.160389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.151852 restraints weight = 10856.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.151774 restraints weight = 13889.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.152587 restraints weight = 11479.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.152887 restraints weight = 8922.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.153093 restraints weight = 8286.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6767  Z= 0.162
  Angle     :  0.643   7.461   9171  Z= 0.335
  Chirality :  0.047   0.171   1010
  Planarity :  0.005   0.058   1192
  Dihedral  :  5.426  53.409    940
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.82 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.53 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.33 (0.26), residues: 422
  loop : -1.74 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  50 
 TYR   0.017   0.002   TYR B 126 
 PHE   0.014   0.002   PHE F 128 
 TRP   0.019   0.001   TRP F 179 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6759)
  covalent geometry    : angle       0.64247 ( 9155)
  SS BOND              : bond        0.00458 (    8)
  SS BOND              : angle       0.99752 (   16)
  hydrogen bonds       : bond        0.03551 (  216)
  hydrogen bonds       : angle       6.16465 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B   62 MET cc_start: 0.7818 (mtt) cc_final: 0.7599 (mtt)
REVERT: B  102 ASP cc_start: 0.7378 (t0) cc_final: 0.7019 (t0)
REVERT: F  232 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9016 (t)
  outliers start: 34
  outliers final: 22
  residues processed: 142
  average time/residue: 0.0737
  time to fit residues: 13.8496
Evaluate side-chains
  137 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  116 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  139 VAL
Chi-restraints excluded: chain F residue  208 VAL
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0570
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
F  53 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.160634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.152082 restraints weight = 10847.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.152231 restraints weight = 11704.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.152771 restraints weight = 9736.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.152912 restraints weight = 8277.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.153003 restraints weight = 7728.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6767  Z= 0.162
  Angle     :  0.666   9.157   9171  Z= 0.343
  Chirality :  0.047   0.177   1010
  Planarity :  0.005   0.057   1192
  Dihedral  :  5.413  51.464    940
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 24.23 %
    Favored  : 70.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.50 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.30 (0.26), residues: 422
  loop : -1.73 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 101 
 TYR   0.020   0.002   TYR E 127 
 PHE   0.014   0.002   PHE F 128 
 TRP   0.019   0.001   TRP F 179 
 HIS   0.004   0.001   HIS E 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6759)
  covalent geometry    : angle       0.66482 ( 9155)
  SS BOND              : bond        0.00442 (    8)
  SS BOND              : angle       0.99289 (   16)
  hydrogen bonds       : bond        0.03531 (  216)
  hydrogen bonds       : angle       6.13662 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 118
  time to evaluate  : 0.160 
Fit side-chains
REVERT: B   62 MET cc_start: 0.7752 (mtt) cc_final: 0.7542 (mtt)
REVERT: B  102 ASP cc_start: 0.7279 (t0) cc_final: 0.7077 (t0)
REVERT: B  240 PHE cc_start: 0.7004 (m-10) cc_final: 0.6602 (m-80)
REVERT: F   58 MET cc_start: 0.3365 (ppp) cc_final: 0.2672 (ttp)
REVERT: F  232 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.8991 (t)
  outliers start: 36
  outliers final: 24
  residues processed: 144
  average time/residue: 0.0690
  time to fit residues: 13.1104
Evaluate side-chains
  141 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  116 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  121 SER
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  139 VAL
Chi-restraints excluded: chain F residue  208 VAL
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.158748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.151140 restraints weight = 10728.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.151072 restraints weight = 10638.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.151490 restraints weight = 10080.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.151704 restraints weight = 8764.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.151875 restraints weight = 7761.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6767  Z= 0.188
  Angle     :  0.693   8.799   9171  Z= 0.360
  Chirality :  0.048   0.185   1010
  Planarity :  0.005   0.059   1192
  Dihedral  :  5.515  48.724    940
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 25.35 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.48 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.33 (0.26), residues: 415
  loop : -1.64 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 101 
 TYR   0.023   0.002   TYR E 127 
 PHE   0.014   0.002   PHE F 128 
 TRP   0.023   0.002   TRP F 179 
 HIS   0.003   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 6759)
  covalent geometry    : angle       0.69152 ( 9155)
  SS BOND              : bond        0.00460 (    8)
  SS BOND              : angle       1.28223 (   16)
  hydrogen bonds       : bond        0.03669 (  216)
  hydrogen bonds       : angle       6.24331 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 0.168 
Fit side-chains
REVERT: B   62 MET cc_start: 0.7840 (mtt) cc_final: 0.7611 (mtt)
REVERT: B  240 PHE cc_start: 0.7033 (m-10) cc_final: 0.6555 (m-80)
REVERT: F   58 MET cc_start: 0.3460 (ppp) cc_final: 0.2805 (ttp)
REVERT: F  232 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9009 (t)
  outliers start: 33
  outliers final: 27
  residues processed: 149
  average time/residue: 0.0823
  time to fit residues: 16.0071
Evaluate side-chains
  138 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   88 GLN
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   63 MET
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  116 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  121 SER
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  139 VAL
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  208 VAL
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    0.2980
   chunk 78 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
F 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.165510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.155234 restraints weight = 10784.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.156561 restraints weight = 7652.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.157612 restraints weight = 5802.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.158206 restraints weight = 4668.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.158715 restraints weight = 3919.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6767  Z= 0.179
  Angle     :  0.690   7.306   9171  Z= 0.360
  Chirality :  0.048   0.181   1010
  Planarity :  0.005   0.060   1192
  Dihedral  :  5.520  46.201    940
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 26.18 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.48 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.32 (0.26), residues: 411
  loop : -1.64 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 154 
 TYR   0.022   0.002   TYR E 127 
 PHE   0.040   0.002   PHE A 235 
 TRP   0.023   0.002   TRP F 179 
 HIS   0.003   0.001   HIS F 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 6759)
  covalent geometry    : angle       0.68806 ( 9155)
  SS BOND              : bond        0.00435 (    8)
  SS BOND              : angle       1.30175 (   16)
  hydrogen bonds       : bond        0.03608 (  216)
  hydrogen bonds       : angle       6.23047 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 116
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.7655 (mtt) cc_final: 0.7449 (mtt)
REVERT: B  240 PHE cc_start: 0.6843 (m-10) cc_final: 0.6419 (m-80)
REVERT: F   58 MET cc_start: 0.3368 (OUTLIER) cc_final: 0.2664 (ttp)
REVERT: F  232 THR cc_start: 0.9317 (OUTLIER) cc_final: 0.9015 (t)
  outliers start: 37
  outliers final: 30
  residues processed: 145
  average time/residue: 0.0813
  time to fit residues: 15.5372
Evaluate side-chains
  140 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   88 GLN
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  105 ARG
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   63 MET
Chi-restraints excluded: chain E residue   68 VAL
Chi-restraints excluded: chain E residue   77 ASN
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  116 VAL
Chi-restraints excluded: chain E residue  152 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   58 MET
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  121 SER
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  139 VAL
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  190 VAL
Chi-restraints excluded: chain F residue  208 VAL
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 77 optimal weight:    0.2980
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.159787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.152790 restraints weight = 10866.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.152664 restraints weight = 11109.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.153125 restraints weight = 10987.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.153377 restraints weight = 8171.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.153480 restraints weight = 7080.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
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      :  0.004   0.033   6767  Z= 0.159
  Angle     :  0.677   7.245   9171  Z= 0.351
  Chirality :  0.047   0.169   1010
  Planarity :  0.004   0.060   1192
  Dihedral  :  5.430  48.125    940
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 26.46 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.46 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.28 (0.26), residues: 410
  loop : -1.65 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 101 
 TYR   0.019   0.002   TYR E 127 
 PHE   0.037   0.002   PHE A 235 
 TRP   0.025   0.002   TRP F 179 
 HIS   0.003   0.001   HIS E 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6759)
  covalent geometry    : angle       0.67259 ( 9155)
  SS BOND              : bond        0.00545 (    8)
  SS BOND              : angle       1.88139 (   16)
  hydrogen bonds       : bond        0.03477 (  216)
  hydrogen bonds       : angle       6.16509 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 113
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 MET cc_start: 0.7863 (mtt) cc_final: 0.7640 (mtt)
REVERT: F   58 MET cc_start: 0.3376 (OUTLIER) cc_final: 0.2777 (ttp)
REVERT: F   63 MET cc_start: 0.5765 (ptp) cc_final: 0.5543 (ptp)
REVERT: F  232 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9038 (t)
  outliers start: 35
  outliers final: 30
  residues processed: 141
  average time/residue: 0.0816
  time to fit residues: 15.2562
Evaluate side-chains
  143 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   88 GLN
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  105 ARG
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   63 MET
Chi-restraints excluded: chain E residue   68 VAL
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  116 VAL
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   58 MET
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  121 SER
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  139 VAL
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  190 VAL
Chi-restraints excluded: chain F residue  208 VAL
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0970
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.160062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.148804 restraints weight = 10972.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.150398 restraints weight = 7729.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.151583 restraints weight = 5767.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.152443 restraints weight = 4522.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.152860 restraints weight = 3721.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6767  Z= 0.151
  Angle     :  0.675   7.636   9171  Z= 0.351
  Chirality :  0.047   0.160   1010
  Planarity :  0.004   0.060   1192
  Dihedral  :  5.203  50.120    938
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.58 %
    Favored  : 67.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.41 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.27 (0.26), residues: 412
  loop : -1.59 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG F 101 
 TYR   0.019   0.002   TYR E 127 
 PHE   0.035   0.002   PHE A 235 
 TRP   0.038   0.002   TRP F 179 
 HIS   0.004   0.001   HIS B 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6759)
  covalent geometry    : angle       0.67156 ( 9155)
  SS BOND              : bond        0.00479 (    8)
  SS BOND              : angle       1.79526 (   16)
  hydrogen bonds       : bond        0.03343 (  216)
  hydrogen bonds       : angle       6.08192 (  555)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.185 
Fit side-chains
REVERT: B   62 MET cc_start: 0.7703 (mtt) cc_final: 0.7498 (mtt)
REVERT: B  102 ASP cc_start: 0.6918 (t0) cc_final: 0.5979 (t0)
REVERT: F   58 MET cc_start: 0.3494 (OUTLIER) cc_final: 0.2700 (ttp)
REVERT: F   63 MET cc_start: 0.5828 (ptp) cc_final: 0.5574 (ptp)
REVERT: F  232 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8973 (t)
  outliers start: 33
  outliers final: 26
  residues processed: 137
  average time/residue: 0.0790
  time to fit residues: 14.4123
Evaluate side-chains
  138 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   96 THR
Chi-restraints excluded: chain A residue  108 VAL
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  216 ASN
Chi-restraints excluded: chain E residue   68 VAL
Chi-restraints excluded: chain E residue   78 VAL
Chi-restraints excluded: chain E residue  116 VAL
Chi-restraints excluded: chain E residue  190 VAL
Chi-restraints excluded: chain E residue  195 VAL
Chi-restraints excluded: chain F residue   58 MET
Chi-restraints excluded: chain F residue   75 VAL
Chi-restraints excluded: chain F residue   78 VAL
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  121 SER
Chi-restraints excluded: chain F residue  129 GLN
Chi-restraints excluded: chain F residue  139 VAL
Chi-restraints excluded: chain F residue  152 VAL
Chi-restraints excluded: chain F residue  232 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0370
   chunk 75 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 80 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.4058

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

Flipped N/Q/H residues before XYZ refinement:
A 156 HIS
** B 156 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 = 0.4077 r_free = 0.4077 target = 0.167001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.159250 restraints weight = 10532.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.159613 restraints weight = 8721.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.159949 restraints weight = 7090.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.160143 restraints weight = 6473.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.160333 restraints weight = 6169.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6767  Z= 0.131
  Angle     :  0.658  11.436   9171  Z= 0.338
  Chirality :  0.047   0.147   1010
  Planarity :  0.005   0.060   1192
  Dihedral  :  5.061  49.044    938
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 27.72 %
    Favored  : 67.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.91 %
    Cis-general     : 0.12 %
    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 are not related in a simple way.
  whole: -1.35 (0.29), residues: 850
  helix:  None (None), residues: 0
  sheet: -0.21 (0.26), residues: 408
  loop : -1.57 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F 101 
 TYR   0.017   0.001   TYR E 127 
 PHE   0.035   0.002   PHE A 235 
 TRP   0.016   0.001   TRP F 179 
 HIS   0.003   0.001   HIS E 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6759)
  covalent geometry    : angle       0.65564 ( 9155)
  SS BOND              : bond        0.00430 (    8)
  SS BOND              : angle       1.50207 (   16)
  hydrogen bonds       : bond        0.03224 (  216)
  hydrogen bonds       : angle       5.95802 (  555)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1185.86 seconds
wall clock time: 21 minutes 7.83 seconds (1267.83 seconds total)