Starting phenix.real_space_refine
on Thu Mar 13 08:13:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xji_22211/03_2025/6xji_22211_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xji_22211/03_2025/6xji_22211.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2025/6xji_22211.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2025/6xji_22211.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2025/6xji_22211_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xji_22211/03_2025/6xji_22211_neut.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      38      5.16       5
     C    5738      2.51       5
     N    1404      2.21       5
     O    1566      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8754
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 2030
          Classifications: {'peptide': 251}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 243}
    Chain: "C"
      Number of atoms: 2315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2315
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 283}
    Chain: "D"
      Number of atoms: 2315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2315
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 283}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'AGS': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.31, per 1000 atoms: 0.72
  Number of scatterers: 8754
  At special positions: 0
  Unit cell: (75.98, 102.18, 132.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      38     16.00
     P       6     15.00
     Mg      2     11.99
     O    1566      8.00
     N    1404      7.00
     C    5738      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 6 sheets defined
      64.0% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid -4 through 15
    Processing helix  chain 'A' and resid 17 through 38
      removed outlier: 3.705A  pdb=" N   TYR A  21 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 80
      removed outlier: 3.562A  pdb=" N   VAL A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   ASP A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 86
    Processing helix  chain 'A' and resid 89 through 126
    Processing helix  chain 'A' and resid 132 through 162
    Processing helix  chain 'A' and resid 164 through 186
      removed outlier: 3.574A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      Proline residue:  A 179  - end of helix
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 191 through 200
      removed outlier: 4.083A  pdb=" N   ASP A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 210
    Processing helix  chain 'A' and resid 211 through 213
      No H-bonds generated for 'chain 'A' and resid 211 through 213'
    Processing helix  chain 'A' and resid 219 through 242
    Processing helix  chain 'B' and resid -3 through 15
    Processing helix  chain 'B' and resid 17 through 38
      removed outlier: 3.705A  pdb=" N   TYR B  21 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 80
      removed outlier: 3.563A  pdb=" N   VAL B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   ASP B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   PHE B  78 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 86
    Processing helix  chain 'B' and resid 89 through 126
    Processing helix  chain 'B' and resid 132 through 162
    Processing helix  chain 'B' and resid 164 through 186
      removed outlier: 3.575A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      Proline residue:  B 179  - end of helix
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 191 through 200
      removed outlier: 4.084A  pdb=" N   ASP B 200 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 210
    Processing helix  chain 'B' and resid 211 through 213
      No H-bonds generated for 'chain 'B' and resid 211 through 213'
    Processing helix  chain 'B' and resid 219 through 242
    Processing helix  chain 'C' and resid 38 through 48
    Processing helix  chain 'C' and resid 79 through 91
    Processing helix  chain 'C' and resid 96 through 108
    Processing helix  chain 'C' and resid 109 through 113
    Processing helix  chain 'C' and resid 116 through 120
    Processing helix  chain 'C' and resid 121 through 135
    Processing helix  chain 'C' and resid 151 through 169
      removed outlier: 4.068A  pdb=" N   ASN C 167 " --> pdb=" O   LYS C 163 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 184
    Processing helix  chain 'C' and resid 218 through 220
      No H-bonds generated for 'chain 'C' and resid 218 through 220'
    Processing helix  chain 'C' and resid 221 through 233
    Processing helix  chain 'C' and resid 240 through 242
      No H-bonds generated for 'chain 'C' and resid 240 through 242'
    Processing helix  chain 'C' and resid 253 through 263
    Processing helix  chain 'C' and resid 276 through 286
    Processing helix  chain 'C' and resid 287 through 289
      No H-bonds generated for 'chain 'C' and resid 287 through 289'
    Processing helix  chain 'D' and resid 38 through 48
    Processing helix  chain 'D' and resid 79 through 91
    Processing helix  chain 'D' and resid 96 through 108
    Processing helix  chain 'D' and resid 109 through 113
    Processing helix  chain 'D' and resid 116 through 120
    Processing helix  chain 'D' and resid 121 through 135
    Processing helix  chain 'D' and resid 151 through 169
      removed outlier: 4.068A  pdb=" N   ASN D 167 " --> pdb=" O   LYS D 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 184
    Processing helix  chain 'D' and resid 218 through 220
      No H-bonds generated for 'chain 'D' and resid 218 through 220'
    Processing helix  chain 'D' and resid 221 through 233
    Processing helix  chain 'D' and resid 253 through 263
    Processing helix  chain 'D' and resid 276 through 286
    Processing helix  chain 'D' and resid 287 through 289
      No H-bonds generated for 'chain 'D' and resid 287 through 289'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 21
      removed outlier: 6.311A  pdb=" N   LYS C   8 " --> pdb=" O   VAL C  15 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ASN C  17 " --> pdb=" O   ILE C   6 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE C   6 " --> pdb=" O   ASN C  17 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ILE C  19 " --> pdb=" O   GLU C   4 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   GLU C   4 " --> pdb=" O   ILE C  19 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   PHE C  21 " --> pdb=" O   LYS C   2 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   LYS C   2 " --> pdb=" O   PHE C  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 68
      removed outlier: 6.437A  pdb=" N   LEU C 141 " --> pdb=" O   LEU C 174 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   SER C 176 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU C 143 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE C  28 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   VAL C 191 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   GLY C  30 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   LEU C 193 " --> pdb=" O   GLY C  30 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE C  32 " --> pdb=" O   LEU C 193 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN C 200 " --> pdb=" O   PHE C 192 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ARG C 194 " --> pdb=" O   PHE C 198 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   PHE C 198 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 235 through 239
      removed outlier: 6.940A  pdb=" N   MET C 246 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   VAL C 238 " --> pdb=" O   HIS C 244 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   HIS C 244 " --> pdb=" O   VAL C 238 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 13 through 21
      removed outlier: 6.310A  pdb=" N   LYS D   8 " --> pdb=" O   VAL D  15 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN D  17 " --> pdb=" O   ILE D   6 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   ILE D   6 " --> pdb=" O   ASN D  17 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ILE D  19 " --> pdb=" O   GLU D   4 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   GLU D   4 " --> pdb=" O   ILE D  19 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   PHE D  21 " --> pdb=" O   LYS D   2 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   LYS D   2 " --> pdb=" O   PHE D  21 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 65 through 68
      removed outlier: 6.436A  pdb=" N   LEU D 141 " --> pdb=" O   LEU D 174 " (cutoff:3.500A)
      removed outlier: 7.779A  pdb=" N   SER D 176 " --> pdb=" O   LEU D 141 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   LEU D 143 " --> pdb=" O   SER D 176 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ILE D  28 " --> pdb=" O   ARG D 189 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   VAL D 191 " --> pdb=" O   ILE D  28 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   GLY D  30 " --> pdb=" O   VAL D 191 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   LEU D 193 " --> pdb=" O   GLY D  30 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ILE D  32 " --> pdb=" O   LEU D 193 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ALA D 190 " --> pdb=" O   ASP D 201 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   ASP D 201 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   PHE D 192 " --> pdb=" O   VAL D 199 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 235 through 239
      removed outlier: 8.510A  pdb=" N   LEU D 235 " --> pdb=" O   ASN D 248 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   ASN D 248 " --> pdb=" O   LEU D 235 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   THR D 212 " --> pdb=" O   ARG D 273 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG D 273 " --> pdb=" O   THR D 212 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TYR D 269 " --> pdb=" O   THR D 216 " (cutoff:3.500A)

    539 hydrogen bonds defined for protein.
    1545 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: 2.56

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 1753
        1.32 -     1.47: 3128
        1.47 -     1.61: 3981
        1.61 -     1.75: 16
        1.75 -     1.90: 56
  Bond restraints: 8934
  Sorted by residual:
  bond pdb=" C   VAL C 199 "
       pdb=" N   GLN C 200 "
    ideal  model  delta    sigma   weight residual
    1.330  1.512 -0.182 1.45e-02 4.76e+03 1.58e+02
  bond pdb=" C   TYR D 266 "
       pdb=" N   PRO D 267 "
    ideal  model  delta    sigma   weight residual
    1.332  1.234  0.098 1.30e-02 5.92e+03 5.67e+01
  bond pdb=" C   ILE C 270 "
       pdb=" N   GLU C 271 "
    ideal  model  delta    sigma   weight residual
    1.331  1.411 -0.080 1.23e-02 6.61e+03 4.20e+01
  bond pdb=" CB  HIS B 115 "
       pdb=" CG  HIS B 115 "
    ideal  model  delta    sigma   weight residual
    1.497  1.407  0.090 1.40e-02 5.10e+03 4.11e+01
  bond pdb=" CB  HIS A 115 "
       pdb=" CG  HIS A 115 "
    ideal  model  delta    sigma   weight residual
    1.497  1.407  0.090 1.40e-02 5.10e+03 4.10e+01
  ... (remaining 8929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 11096
        2.68 -     5.35: 855
        5.35 -     8.03: 106
        8.03 -    10.71: 14
       10.71 -    13.39: 9
  Bond angle restraints: 12080
  Sorted by residual:
  angle pdb=" O   ILE C 270 "
        pdb=" C   ILE C 270 "
        pdb=" N   GLU C 271 "
      ideal   model   delta    sigma   weight residual
     123.00  111.71   11.29 1.10e+00 8.26e-01 1.05e+02
  angle pdb=" O   VAL C 215 "
        pdb=" C   VAL C 215 "
        pdb=" N   THR C 216 "
      ideal   model   delta    sigma   weight residual
     123.10  112.21   10.89 1.17e+00 7.31e-01 8.67e+01
  angle pdb=" CA  ILE C 270 "
        pdb=" C   ILE C 270 "
        pdb=" N   GLU C 271 "
      ideal   model   delta    sigma   weight residual
     115.75  127.43  -11.68 1.28e+00 6.10e-01 8.33e+01
  angle pdb=" CA  VAL C 215 "
        pdb=" C   VAL C 215 "
        pdb=" N   THR C 216 "
      ideal   model   delta    sigma   weight residual
     116.34  127.05  -10.71 1.28e+00 6.10e-01 7.00e+01
  angle pdb=" C   VAL C 215 "
        pdb=" N   THR C 216 "
        pdb=" CA  THR C 216 "
      ideal   model   delta    sigma   weight residual
     123.00  133.79  -10.79 1.38e+00 5.25e-01 6.11e+01
  ... (remaining 12075 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.45: 5162
       22.45 -    44.89: 134
       44.89 -    67.34: 32
       67.34 -    89.78: 12
       89.78 -   112.23: 2
  Dihedral angle restraints: 5342
    sinusoidal: 2174
      harmonic: 3168
  Sorted by residual:
  dihedral pdb=" O1A AGS C 301 "
           pdb=" O3A AGS C 301 "
           pdb=" PA  AGS C 301 "
           pdb=" PB  AGS C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   44.50 -112.23     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" O1A AGS D 301 "
           pdb=" O3A AGS D 301 "
           pdb=" PA  AGS D 301 "
           pdb=" PB  AGS D 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -67.73   44.46 -112.19     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" C   ILE B 188 "
           pdb=" N   ILE B 188 "
           pdb=" CA  ILE B 188 "
           pdb=" CB  ILE B 188 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.51    8.51     0      2.50e+00 1.60e-01 1.16e+01
  ... (remaining 5339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 808
       0.067 -    0.134: 420
       0.134 -    0.201: 130
       0.201 -    0.268: 40
       0.268 -    0.335: 12
  Chirality restraints: 1410
  Sorted by residual:
  chirality pdb=" CB  VAL D 166 "
            pdb=" CA  VAL D 166 "
            pdb=" CG1 VAL D 166 "
            pdb=" CG2 VAL D 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CB  VAL C 166 "
            pdb=" CA  VAL C 166 "
            pdb=" CG1 VAL C 166 "
            pdb=" CG2 VAL C 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CA  THR D 272 "
            pdb=" N   THR D 272 "
            pdb=" C   THR D 272 "
            pdb=" CB  THR D 272 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.86   -0.33 2.00e-01 2.50e+01 2.75e+00
  ... (remaining 1407 not shown)

  Planarity restraints: 1472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 206 "   -0.069 2.00e-02 2.50e+03   3.63e-02 2.63e+01
        pdb=" CG  TYR B 206 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 206 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 206 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 206 "    0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 206 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 206 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 206 "   -0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 206 "    0.068 2.00e-02 2.50e+03   3.61e-02 2.61e+01
        pdb=" CG  TYR A 206 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 206 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 206 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 206 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 206 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 206 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 212 "   -0.021 2.00e-02 2.50e+03   4.42e-02 1.95e+01
        pdb=" C   THR D 212 "    0.076 2.00e-02 2.50e+03
        pdb=" O   THR D 212 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   THR D 213 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1469 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 851
        2.72 -     3.26: 9261
        3.26 -     3.81: 14509
        3.81 -     4.35: 18585
        4.35 -     4.90: 30145
  Nonbonded interactions: 73351
  Sorted by model distance:
  nonbonded pdb=" O2G AGS D 301 "
            pdb="MG    MG D 302 "
     model   vdw
     2.173 2.170
  nonbonded pdb=" O2G AGS C 301 "
            pdb="MG    MG C 302 "
     model   vdw
     2.173 2.170
  nonbonded pdb=" CG2 THR D 212 "
            pdb=" OE1 GLN D 236 "
     model   vdw
     2.188 3.460
  nonbonded pdb=" N   LYS D  39 "
            pdb=" O1B AGS D 301 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" N   LYS C  39 "
            pdb=" O1B AGS C 301 "
     model   vdw
     2.258 3.120
  ... (remaining 73346 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.470
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5998
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      :  0.018   0.182   8934  Z= 1.190
  Angle     :  1.602  13.386  12080  Z= 1.098
  Chirality :  0.092   0.335   1410
  Planarity :  0.008   0.044   1472
  Dihedral  : 12.076 112.230   3298
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  1.86 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.24), residues: 1074
  helix:  1.19 (0.19), residues: 606
  sheet:  0.91 (0.57), residues: 87
  loop : -0.06 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.007   TRP A 223 
 HIS   0.009   0.003   HIS C 232 
 PHE   0.030   0.005   PHE B  55 
 TYR   0.069   0.008   TYR B 206 
 ARG   0.011   0.001   ARG C 189 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 385
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 LYS cc_start: 0.7717 (mttt) cc_final: 0.7006 (ttpp)
REVERT: A   51 TYR cc_start: 0.7737 (m-80) cc_final: 0.7352 (m-80)
REVERT: A   83 ILE cc_start: 0.7062 (tt) cc_final: 0.5957 (tt)
REVERT: A  162 GLN cc_start: 0.7683 (mt0) cc_final: 0.7314 (pt0)
REVERT: A  166 MET cc_start: 0.6175 (mmp) cc_final: 0.4576 (ttm)
REVERT: B   16 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7079 (ttpt)
REVERT: B   99 SER cc_start: 0.8641 (t) cc_final: 0.8339 (m)
REVERT: B  116 TYR cc_start: 0.6612 (t80) cc_final: 0.5797 (t80)
REVERT: B  122 VAL cc_start: 0.8149 (t) cc_final: 0.7750 (t)
REVERT: B  142 PHE cc_start: 0.8493 (t80) cc_final: 0.8290 (t80)
REVERT: B  166 MET cc_start: 0.6704 (mmp) cc_final: 0.6450 (mmm)
REVERT: B  211 MET cc_start: 0.8622 (mtp) cc_final: 0.8337 (ptp)
REVERT: C    5 HIS cc_start: 0.5984 (m-70) cc_final: 0.5356 (m90)
REVERT: C   13 ASN cc_start: 0.6712 (t0) cc_final: 0.6451 (t0)
REVERT: C   18 ASP cc_start: 0.7170 (t0) cc_final: 0.6827 (m-30)
REVERT: C   20 ASP cc_start: 0.7347 (m-30) cc_final: 0.6763 (t70)
REVERT: C   43 MET cc_start: 0.8065 (mtm) cc_final: 0.7744 (mtp)
REVERT: C   58 ASP cc_start: 0.7313 (t0) cc_final: 0.6994 (m-30)
REVERT: C  105 ASP cc_start: 0.8347 (m-30) cc_final: 0.7856 (p0)
REVERT: C  118 LYS cc_start: 0.8294 (pttt) cc_final: 0.7879 (tptt)
REVERT: C  135 MET cc_start: 0.7637 (mmm) cc_final: 0.7215 (mmt)
REVERT: C  195 ASP cc_start: 0.6927 (m-30) cc_final: 0.6680 (m-30)
REVERT: D    1 MET cc_start: 0.3952 (tpp) cc_final: 0.3705 (mmm)
REVERT: D   56 LYS cc_start: 0.5901 (tttt) cc_final: 0.5669 (tptm)
REVERT: D   77 ASN cc_start: 0.8150 (p0) cc_final: 0.7079 (m-40)
REVERT: D  165 LEU cc_start: 0.8255 (mt) cc_final: 0.8033 (mt)
REVERT: D  181 GLU cc_start: 0.7113 (mp0) cc_final: 0.6607 (tt0)
REVERT: D  273 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6499 (ttm110)
REVERT: D  281 TYR cc_start: 0.5233 (t80) cc_final: 0.4838 (t80)
  outliers start: 7
  outliers final: 2
  residues processed: 388
  average time/residue: 0.2183
  time to fit residues: 114.0945
Evaluate side-chains
  215 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 212
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  271 GLU
Chi-restraints excluded: chain D residue  273 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C 219 HIS
C 237 ASN
D   5 HIS
D  35 ASN
** D  83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 203 ASN
D 285 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.172589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.148607 restraints weight = 11893.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.151404 restraints weight = 8072.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.152969 restraints weight = 6086.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   8934  Z= 0.242
  Angle     :  0.708   9.859  12080  Z= 0.381
  Chirality :  0.047   0.314   1410
  Planarity :  0.004   0.032   1472
  Dihedral  : 10.313 122.711   1205
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 11.65 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.25), residues: 1074
  helix:  2.07 (0.20), residues: 602
  sheet:  0.97 (0.59), residues: 86
  loop : -0.43 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP B 223 
 HIS   0.007   0.001   HIS C 244 
 PHE   0.040   0.002   PHE C 107 
 TYR   0.025   0.002   TYR A 206 
 ARG   0.004   0.001   ARG C 224 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 245
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.7122 (m-80) cc_final: 0.6849 (m-80)
REVERT: A  166 MET cc_start: 0.6134 (mmp) cc_final: 0.4845 (ttm)
REVERT: B   11 LEU cc_start: 0.8782 (mt) cc_final: 0.8577 (mt)
REVERT: B   68 MET cc_start: 0.8359 (mmm) cc_final: 0.7955 (mmp)
REVERT: B  116 TYR cc_start: 0.7185 (t80) cc_final: 0.6588 (t80)
REVERT: B  144 LEU cc_start: 0.8631 (mt) cc_final: 0.8389 (tt)
REVERT: B  239 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8331 (tt)
REVERT: C    5 HIS cc_start: 0.5196 (m-70) cc_final: 0.4790 (m90)
REVERT: C   77 ASN cc_start: 0.7744 (m110) cc_final: 0.7436 (m110)
REVERT: C   89 GLN cc_start: 0.8017 (mt0) cc_final: 0.7532 (mt0)
REVERT: C  124 MET cc_start: 0.8325 (mtm) cc_final: 0.8043 (mtm)
REVERT: C  135 MET cc_start: 0.7555 (mmm) cc_final: 0.7272 (mmt)
REVERT: C  222 PHE cc_start: 0.5140 (t80) cc_final: 0.4245 (t80)
REVERT: C  229 LEU cc_start: 0.5878 (mp) cc_final: 0.5642 (mp)
REVERT: C  245 LEU cc_start: 0.5937 (mt) cc_final: 0.5453 (tt)
REVERT: D   77 ASN cc_start: 0.7230 (p0) cc_final: 0.6603 (m-40)
REVERT: D  100 THR cc_start: 0.7422 (m) cc_final: 0.6957 (m)
REVERT: D  165 LEU cc_start: 0.8413 (mt) cc_final: 0.8184 (mt)
  outliers start: 34
  outliers final: 22
  residues processed: 264
  average time/residue: 0.1905
  time to fit residues: 70.0662
Evaluate side-chains
  211 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  233 PHE
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  271 GLU
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 84 optimal weight:    0.1980
   chunk 66 optimal weight:    2.9990
   chunk 43 optimal weight:    0.2980
   chunk 73 optimal weight:    8.9990
   chunk 97 optimal weight:    3.9990
   chunk 70 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 254 GLN
D   5 HIS
D  35 ASN
D  89 GLN
D 148 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.164619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.140942 restraints weight = 12337.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.143463 restraints weight = 8550.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.145101 restraints weight = 6516.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.4403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8934  Z= 0.214
  Angle     :  0.625  11.510  12080  Z= 0.334
  Chirality :  0.044   0.234   1410
  Planarity :  0.004   0.035   1472
  Dihedral  :  9.848 114.174   1201
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 15.57 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1074
  helix:  2.01 (0.20), residues: 605
  sheet:  0.52 (0.57), residues: 86
  loop : -0.81 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 223 
 HIS   0.005   0.001   HIS D 244 
 PHE   0.028   0.002   PHE C 107 
 TYR   0.026   0.001   TYR B  51 
 ARG   0.005   0.001   ARG D 224 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 217
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.7288 (m-80) cc_final: 0.6948 (m-80)
REVERT: A  166 MET cc_start: 0.6223 (mmp) cc_final: 0.5095 (ttm)
REVERT: B   11 LEU cc_start: 0.8908 (mt) cc_final: 0.8677 (mt)
REVERT: B  110 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8043 (tt)
REVERT: B  116 TYR cc_start: 0.7391 (t80) cc_final: 0.6906 (t80)
REVERT: B  222 GLN cc_start: 0.7655 (tt0) cc_final: 0.7354 (mt0)
REVERT: B  239 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8381 (tp)
REVERT: C   37 VAL cc_start: 0.9060 (p) cc_final: 0.8793 (m)
REVERT: C   82 TYR cc_start: 0.7132 (t80) cc_final: 0.6876 (t80)
REVERT: C   89 GLN cc_start: 0.8258 (mt0) cc_final: 0.7989 (mt0)
REVERT: C  150 MET cc_start: 0.7883 (mtp) cc_final: 0.7496 (mtm)
REVERT: D    5 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.7048 (m-70)
REVERT: D   35 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7489 (p0)
REVERT: D   37 VAL cc_start: 0.8781 (p) cc_final: 0.8536 (p)
REVERT: D   77 ASN cc_start: 0.7257 (p0) cc_final: 0.6957 (m-40)
REVERT: D  135 MET cc_start: 0.8461 (mmt) cc_final: 0.8204 (mmm)
REVERT: D  193 LEU cc_start: 0.8258 (tt) cc_final: 0.7886 (mp)
REVERT: D  263 LEU cc_start: 0.5293 (tp) cc_final: 0.4991 (mp)
  outliers start: 43
  outliers final: 25
  residues processed: 244
  average time/residue: 0.1799
  time to fit residues: 62.3816
Evaluate side-chains
  214 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   42 MET
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   20 ASP
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  214 ILE
Chi-restraints excluded: chain D residue    5 HIS
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.2980
   chunk 60 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   chunk 50 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
D   5 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.165981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.143102 restraints weight = 12168.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.145553 restraints weight = 8355.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.147229 restraints weight = 6375.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.4852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8934  Z= 0.232
  Angle     :  0.624  10.198  12080  Z= 0.329
  Chirality :  0.044   0.351   1410
  Planarity :  0.004   0.039   1472
  Dihedral  :  9.344 116.179   1198
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 16.39 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.25), residues: 1074
  helix:  1.83 (0.20), residues: 605
  sheet: -0.12 (0.53), residues: 95
  loop : -0.85 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 223 
 HIS   0.013   0.001   HIS D   5 
 PHE   0.040   0.002   PHE C 107 
 TYR   0.021   0.001   TYR A 206 
 ARG   0.003   0.000   ARG C 172 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 201
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.7312 (m-80) cc_final: 0.6998 (m-80)
REVERT: A  166 MET cc_start: 0.6094 (mmp) cc_final: 0.4924 (ttm)
REVERT: B   11 LEU cc_start: 0.8921 (mt) cc_final: 0.8643 (mt)
REVERT: B   80 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7828 (mm-40)
REVERT: B  110 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8128 (tt)
REVERT: B  116 TYR cc_start: 0.7368 (t80) cc_final: 0.6937 (t80)
REVERT: B  222 GLN cc_start: 0.7611 (tt0) cc_final: 0.7314 (mt0)
REVERT: B  239 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8407 (tp)
REVERT: C   37 VAL cc_start: 0.9082 (p) cc_final: 0.8792 (m)
REVERT: C   43 MET cc_start: 0.7284 (mtm) cc_final: 0.6577 (mmm)
REVERT: C   82 TYR cc_start: 0.7117 (t80) cc_final: 0.6826 (t80)
REVERT: C   89 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7929 (mt0)
REVERT: C   99 TYR cc_start: 0.7416 (t80) cc_final: 0.7068 (t80)
REVERT: C  135 MET cc_start: 0.7316 (mmt) cc_final: 0.6964 (mmp)
REVERT: D    2 LYS cc_start: 0.8455 (mttp) cc_final: 0.6696 (ptmt)
REVERT: D  135 MET cc_start: 0.8358 (mmt) cc_final: 0.8146 (mmm)
REVERT: D  194 ARG cc_start: 0.7759 (tmt170) cc_final: 0.6780 (tmm-80)
REVERT: D  195 ASP cc_start: 0.8089 (m-30) cc_final: 0.7610 (m-30)
REVERT: D  200 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6988 (tm-30)
  outliers start: 47
  outliers final: 37
  residues processed: 227
  average time/residue: 0.1601
  time to fit residues: 52.9087
Evaluate side-chains
  224 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 184
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  210 LYS
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  176 SER
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 66 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C 148 ASN
C 285 ASN
D  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.161872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.138945 restraints weight = 12164.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.141310 restraints weight = 8327.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.142881 restraints weight = 6350.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.5180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8934  Z= 0.190
  Angle     :  0.584   7.929  12080  Z= 0.310
  Chirality :  0.043   0.328   1410
  Planarity :  0.004   0.035   1472
  Dihedral  :  9.081 115.696   1198
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 17.73 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1074
  helix:  1.77 (0.20), residues: 609
  sheet: -0.19 (0.53), residues: 95
  loop : -0.94 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 223 
 HIS   0.006   0.001   HIS D 244 
 PHE   0.037   0.002   PHE C 107 
 TYR   0.021   0.001   TYR A 206 
 ARG   0.011   0.001   ARG A 190 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 203
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 TYR cc_start: 0.8040 (m-80) cc_final: 0.7682 (t80)
REVERT: A   38 MET cc_start: 0.6293 (mpp) cc_final: 0.6005 (mmp)
REVERT: A   51 TYR cc_start: 0.7052 (m-80) cc_final: 0.6835 (m-80)
REVERT: A  166 MET cc_start: 0.5954 (mmp) cc_final: 0.4562 (ttm)
REVERT: B    2 ARG cc_start: 0.6561 (mtm-85) cc_final: 0.5865 (tmt170)
REVERT: B   11 LEU cc_start: 0.8878 (mt) cc_final: 0.8617 (mt)
REVERT: B   68 MET cc_start: 0.8563 (mmp) cc_final: 0.8249 (mmt)
REVERT: B   80 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7807 (mm-40)
REVERT: B  110 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8103 (tt)
REVERT: B  116 TYR cc_start: 0.7486 (t80) cc_final: 0.6844 (t80)
REVERT: B  222 GLN cc_start: 0.7602 (tt0) cc_final: 0.7390 (mt0)
REVERT: B  239 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8351 (tp)
REVERT: C   37 VAL cc_start: 0.9032 (p) cc_final: 0.8725 (m)
REVERT: C   43 MET cc_start: 0.7303 (mtm) cc_final: 0.7056 (mtm)
REVERT: C   82 TYR cc_start: 0.7166 (t80) cc_final: 0.6797 (t80)
REVERT: C   89 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7849 (mt0)
REVERT: C   99 TYR cc_start: 0.7439 (t80) cc_final: 0.7175 (t80)
REVERT: C  107 PHE cc_start: 0.7658 (m-80) cc_final: 0.7373 (m-80)
REVERT: C  135 MET cc_start: 0.7425 (mmt) cc_final: 0.7155 (mmp)
REVERT: D  150 MET cc_start: 0.7603 (mmm) cc_final: 0.7258 (mmm)
REVERT: D  165 LEU cc_start: 0.8149 (mt) cc_final: 0.7396 (mm)
REVERT: D  193 LEU cc_start: 0.8154 (tt) cc_final: 0.7852 (mp)
REVERT: D  194 ARG cc_start: 0.7721 (tmt170) cc_final: 0.6603 (tmm-80)
REVERT: D  195 ASP cc_start: 0.8126 (m-30) cc_final: 0.7618 (m-30)
REVERT: D  200 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7062 (tm-30)
REVERT: D  246 MET cc_start: 0.6221 (mpp) cc_final: 0.5489 (mpp)
REVERT: D  263 LEU cc_start: 0.6306 (mp) cc_final: 0.6068 (tt)
  outliers start: 48
  outliers final: 36
  residues processed: 230
  average time/residue: 0.1771
  time to fit residues: 58.4208
Evaluate side-chains
  220 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 181
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  103 ILE
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0570
   chunk 103 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.160593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.138752 restraints weight = 12391.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.141130 restraints weight = 8273.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.142577 restraints weight = 6160.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.5449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8934  Z= 0.177
  Angle     :  0.581   8.291  12080  Z= 0.307
  Chirality :  0.042   0.242   1410
  Planarity :  0.003   0.034   1472
  Dihedral  :  8.818 114.930   1198
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 19.38 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), residues: 1074
  helix:  1.81 (0.20), residues: 609
  sheet: -0.08 (0.53), residues: 95
  loop : -0.96 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 223 
 HIS   0.005   0.001   HIS D 244 
 PHE   0.027   0.001   PHE C 107 
 TYR   0.022   0.001   TYR A 206 
 ARG   0.004   0.000   ARG A 190 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 192
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.6091 (mpp) cc_final: 0.5852 (mmp)
REVERT: A   51 TYR cc_start: 0.7253 (m-80) cc_final: 0.6976 (m-80)
REVERT: A  166 MET cc_start: 0.6005 (mmp) cc_final: 0.4632 (ttm)
REVERT: B   11 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8478 (mt)
REVERT: B   38 MET cc_start: 0.5560 (tpt) cc_final: 0.4994 (tpt)
REVERT: B   80 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7707 (mm-40)
REVERT: B  110 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7933 (tt)
REVERT: B  116 TYR cc_start: 0.7365 (t80) cc_final: 0.6751 (t80)
REVERT: B  239 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8349 (tp)
REVERT: C   37 VAL cc_start: 0.9015 (p) cc_final: 0.8730 (m)
REVERT: C   43 MET cc_start: 0.7185 (mtm) cc_final: 0.6905 (mtm)
REVERT: C   89 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7889 (mt0)
REVERT: C   99 TYR cc_start: 0.7284 (t80) cc_final: 0.6854 (t80)
REVERT: C  135 MET cc_start: 0.7430 (mmt) cc_final: 0.7153 (mmp)
REVERT: C  189 ARG cc_start: 0.7563 (ptt180) cc_final: 0.7342 (ptt180)
REVERT: C  213 THR cc_start: 0.7069 (m) cc_final: 0.6630 (p)
REVERT: C  221 ASP cc_start: 0.4484 (m-30) cc_final: 0.3786 (p0)
REVERT: D  193 LEU cc_start: 0.8136 (tt) cc_final: 0.7875 (mp)
REVERT: D  194 ARG cc_start: 0.7699 (tmt170) cc_final: 0.6569 (tmm-80)
REVERT: D  195 ASP cc_start: 0.8127 (m-30) cc_final: 0.7612 (m-30)
REVERT: D  200 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: D  246 MET cc_start: 0.5965 (mpp) cc_final: 0.5305 (mpp)
  outliers start: 47
  outliers final: 36
  residues processed: 222
  average time/residue: 0.1748
  time to fit residues: 56.3640
Evaluate side-chains
  217 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 177
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 ILE
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  157 ASP
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain D residue   14 VAL
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  176 SER
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 73 optimal weight:    9.9990
   chunk 10 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   chunk 104 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.159630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.137553 restraints weight = 12504.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.139912 restraints weight = 8441.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.141354 restraints weight = 6261.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.5636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8934  Z= 0.189
  Angle     :  0.590   8.032  12080  Z= 0.309
  Chirality :  0.042   0.202   1410
  Planarity :  0.003   0.035   1472
  Dihedral  :  8.699 114.270   1198
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 19.59 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.25), residues: 1074
  helix:  1.83 (0.20), residues: 611
  sheet:  0.11 (0.52), residues: 100
  loop : -0.94 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 223 
 HIS   0.005   0.001   HIS D 244 
 PHE   0.041   0.002   PHE C 107 
 TYR   0.021   0.001   TYR A 206 
 ARG   0.002   0.000   ARG A  76 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 191
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.7242 (m-80) cc_final: 0.6964 (m-80)
REVERT: A  166 MET cc_start: 0.6136 (mmp) cc_final: 0.4600 (ttm)
REVERT: B    2 ARG cc_start: 0.6565 (mtm-85) cc_final: 0.6080 (tmt170)
REVERT: B   11 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8412 (mt)
REVERT: B   80 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7944 (mm-40)
REVERT: B  110 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7960 (tt)
REVERT: B  116 TYR cc_start: 0.7374 (t80) cc_final: 0.6726 (t80)
REVERT: B  166 MET cc_start: 0.6723 (mmm) cc_final: 0.5853 (mmt)
REVERT: B  232 ILE cc_start: 0.7967 (mp) cc_final: 0.7622 (mt)
REVERT: B  239 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8302 (tp)
REVERT: C   43 MET cc_start: 0.7181 (mtm) cc_final: 0.6912 (mtm)
REVERT: C   89 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7868 (mt0)
REVERT: C   99 TYR cc_start: 0.7474 (t80) cc_final: 0.7148 (t80)
REVERT: C  135 MET cc_start: 0.7403 (mmt) cc_final: 0.6761 (mmt)
REVERT: C  189 ARG cc_start: 0.7599 (ptt180) cc_final: 0.7284 (ptt180)
REVERT: C  213 THR cc_start: 0.7046 (m) cc_final: 0.6615 (p)
REVERT: C  221 ASP cc_start: 0.4527 (m-30) cc_final: 0.3816 (p0)
REVERT: D    2 LYS cc_start: 0.8447 (mttp) cc_final: 0.6674 (ptmm)
REVERT: D  150 MET cc_start: 0.7379 (mmm) cc_final: 0.6554 (mmm)
REVERT: D  165 LEU cc_start: 0.8016 (mt) cc_final: 0.7635 (mm)
REVERT: D  193 LEU cc_start: 0.8115 (tt) cc_final: 0.7877 (mp)
REVERT: D  194 ARG cc_start: 0.7688 (tmt170) cc_final: 0.6826 (tmm-80)
REVERT: D  200 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7061 (tm-30)
REVERT: D  246 MET cc_start: 0.5985 (mpp) cc_final: 0.5698 (mpp)
REVERT: D  263 LEU cc_start: 0.5863 (mp) cc_final: 0.5412 (tp)
  outliers start: 50
  outliers final: 40
  residues processed: 220
  average time/residue: 0.1737
  time to fit residues: 55.1233
Evaluate side-chains
  221 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 177
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  150 MET
Chi-restraints excluded: chain C residue  157 ASP
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  103 ILE
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  176 SER
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 61 optimal weight:    0.3980
   chunk 71 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.160329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.138409 restraints weight = 12564.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.140703 restraints weight = 8406.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.142442 restraints weight = 6263.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8934  Z= 0.189
  Angle     :  0.588   8.751  12080  Z= 0.309
  Chirality :  0.043   0.340   1410
  Planarity :  0.003   0.034   1472
  Dihedral  :  8.559 112.403   1198
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 21.44 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.25), residues: 1074
  helix:  1.86 (0.20), residues: 609
  sheet:  0.16 (0.53), residues: 100
  loop : -0.90 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 223 
 HIS   0.004   0.001   HIS D 244 
 PHE   0.046   0.001   PHE C 107 
 TYR   0.026   0.002   TYR D  75 
 ARG   0.003   0.000   ARG A  76 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 186
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 TYR cc_start: 0.7905 (m-80) cc_final: 0.7572 (t80)
REVERT: A   51 TYR cc_start: 0.7259 (m-80) cc_final: 0.7025 (m-80)
REVERT: A  150 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8310 (m-80)
REVERT: A  166 MET cc_start: 0.6214 (mmp) cc_final: 0.4705 (ttm)
REVERT: B    2 ARG cc_start: 0.6491 (mtm-85) cc_final: 0.6029 (tmt170)
REVERT: B   11 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8306 (mt)
REVERT: B  116 TYR cc_start: 0.7386 (t80) cc_final: 0.6754 (t80)
REVERT: B  239 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8356 (tp)
REVERT: C   43 MET cc_start: 0.7143 (mtm) cc_final: 0.6889 (mtm)
REVERT: C   89 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7828 (mt0)
REVERT: C   99 TYR cc_start: 0.7598 (t80) cc_final: 0.7341 (t80)
REVERT: C  135 MET cc_start: 0.7374 (mmt) cc_final: 0.7054 (mmp)
REVERT: C  189 ARG cc_start: 0.7611 (ptt180) cc_final: 0.7374 (ptt-90)
REVERT: C  213 THR cc_start: 0.7030 (m) cc_final: 0.6595 (p)
REVERT: C  221 ASP cc_start: 0.4841 (m-30) cc_final: 0.4023 (p0)
REVERT: D    2 LYS cc_start: 0.8354 (mttp) cc_final: 0.6697 (ptmm)
REVERT: D  150 MET cc_start: 0.7361 (mmm) cc_final: 0.6436 (mmm)
REVERT: D  165 LEU cc_start: 0.8114 (mt) cc_final: 0.7770 (mm)
REVERT: D  193 LEU cc_start: 0.8117 (tt) cc_final: 0.7899 (mp)
REVERT: D  194 ARG cc_start: 0.7695 (tmt170) cc_final: 0.6812 (tmm-80)
REVERT: D  200 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7108 (tm-30)
REVERT: D  263 LEU cc_start: 0.5999 (mp) cc_final: 0.5548 (tp)
  outliers start: 43
  outliers final: 35
  residues processed: 212
  average time/residue: 0.2348
  time to fit residues: 74.1084
Evaluate side-chains
  219 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 180
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  150 MET
Chi-restraints excluded: chain C residue  157 ASP
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  103 ILE
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  176 SER
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 99 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.158989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.137111 restraints weight = 12611.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.139188 restraints weight = 8494.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.140953 restraints weight = 6442.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.5936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8934  Z= 0.207
  Angle     :  0.613   9.320  12080  Z= 0.320
  Chirality :  0.044   0.339   1410
  Planarity :  0.003   0.036   1472
  Dihedral  :  8.520 110.981   1198
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 21.55 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.25), residues: 1074
  helix:  1.86 (0.20), residues: 609
  sheet:  0.09 (0.53), residues: 100
  loop : -0.95 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 223 
 HIS   0.007   0.001   HIS D 244 
 PHE   0.037   0.001   PHE C 107 
 TYR   0.021   0.001   TYR A 206 
 ARG   0.004   0.000   ARG C 110 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 187
  time to evaluate  : 1.765 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.7366 (m-80) cc_final: 0.7133 (m-80)
REVERT: A  150 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8395 (m-80)
REVERT: A  166 MET cc_start: 0.6236 (mmp) cc_final: 0.4726 (ttm)
REVERT: B    2 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.6014 (tmt170)
REVERT: B   11 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8332 (mt)
REVERT: B  116 TYR cc_start: 0.7430 (t80) cc_final: 0.6846 (t80)
REVERT: B  239 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8361 (tp)
REVERT: C   43 MET cc_start: 0.7133 (mtm) cc_final: 0.6897 (mtm)
REVERT: C   89 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7921 (mt0)
REVERT: C   99 TYR cc_start: 0.7595 (t80) cc_final: 0.7335 (t80)
REVERT: C  189 ARG cc_start: 0.7713 (ptt180) cc_final: 0.7448 (ptt-90)
REVERT: C  213 THR cc_start: 0.7037 (m) cc_final: 0.6608 (p)
REVERT: C  221 ASP cc_start: 0.4762 (m-30) cc_final: 0.3967 (p0)
REVERT: D    2 LYS cc_start: 0.8386 (mttp) cc_final: 0.6680 (ptmm)
REVERT: D  150 MET cc_start: 0.7380 (mmm) cc_final: 0.6411 (mmm)
REVERT: D  165 LEU cc_start: 0.8068 (mt) cc_final: 0.7727 (mm)
REVERT: D  194 ARG cc_start: 0.7743 (tmt170) cc_final: 0.6967 (tmm-80)
REVERT: D  200 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7223 (tm-30)
REVERT: D  221 ASP cc_start: 0.4703 (m-30) cc_final: 0.4173 (m-30)
REVERT: D  246 MET cc_start: 0.6514 (mpp) cc_final: 0.5785 (mpp)
REVERT: D  263 LEU cc_start: 0.6016 (mp) cc_final: 0.5570 (tp)
  outliers start: 47
  outliers final: 40
  residues processed: 213
  average time/residue: 0.2225
  time to fit residues: 68.0252
Evaluate side-chains
  227 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 183
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  114 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  150 MET
Chi-restraints excluded: chain C residue  157 ASP
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  103 ILE
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  176 SER
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 105 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 107 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0470
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.159705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.137439 restraints weight = 12521.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.139788 restraints weight = 8387.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.141489 restraints weight = 6242.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.6084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8934  Z= 0.194
  Angle     :  0.603   9.412  12080  Z= 0.317
  Chirality :  0.044   0.349   1410
  Planarity :  0.003   0.033   1472
  Dihedral  :  8.399 108.812   1198
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 22.37 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1074
  helix:  1.89 (0.20), residues: 609
  sheet:  0.06 (0.54), residues: 100
  loop : -0.96 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 223 
 HIS   0.006   0.001   HIS D 244 
 PHE   0.040   0.002   PHE C 107 
 TYR   0.022   0.001   TYR A 206 
 ARG   0.003   0.000   ARG C 110 

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 188
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.7463 (m-80) cc_final: 0.7245 (m-80)
REVERT: A  150 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8337 (m-80)
REVERT: A  166 MET cc_start: 0.6193 (mmp) cc_final: 0.5942 (tpp)
REVERT: B    2 ARG cc_start: 0.6644 (mtm-85) cc_final: 0.5913 (tmt170)
REVERT: B  116 TYR cc_start: 0.7449 (t80) cc_final: 0.6758 (t80)
REVERT: B  239 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8332 (tp)
REVERT: C   43 MET cc_start: 0.7100 (mtm) cc_final: 0.6851 (mtm)
REVERT: C   89 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7844 (mt0)
REVERT: C  189 ARG cc_start: 0.7686 (ptt180) cc_final: 0.7407 (ptt-90)
REVERT: C  213 THR cc_start: 0.7015 (m) cc_final: 0.6584 (p)
REVERT: C  221 ASP cc_start: 0.4703 (m-30) cc_final: 0.3997 (p0)
REVERT: D    2 LYS cc_start: 0.8364 (mttp) cc_final: 0.6665 (ptmm)
REVERT: D  150 MET cc_start: 0.7391 (mmm) cc_final: 0.6670 (mmm)
REVERT: D  165 LEU cc_start: 0.8034 (mt) cc_final: 0.7728 (mm)
REVERT: D  187 CYS cc_start: 0.6954 (p) cc_final: 0.6684 (m)
REVERT: D  200 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7201 (tm-30)
REVERT: D  221 ASP cc_start: 0.4274 (m-30) cc_final: 0.3923 (m-30)
REVERT: D  246 MET cc_start: 0.6570 (mpp) cc_final: 0.5930 (mpp)
REVERT: D  263 LEU cc_start: 0.6102 (mp) cc_final: 0.5671 (tp)
  outliers start: 43
  outliers final: 38
  residues processed: 216
  average time/residue: 0.2392
  time to fit residues: 75.8209
Evaluate side-chains
  218 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 177
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  150 PHE
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   65 ILE
Chi-restraints excluded: chain C residue   89 GLN
Chi-restraints excluded: chain C residue  150 MET
Chi-restraints excluded: chain C residue  157 ASP
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  176 SER
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain D residue   79 SER
Chi-restraints excluded: chain D residue  103 ILE
Chi-restraints excluded: chain D residue  104 ILE
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  176 SER
Chi-restraints excluded: chain D residue  203 ASN
Chi-restraints excluded: chain D residue  216 THR
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  272 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 95 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0050
   chunk 31 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D  71 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.158899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.137098 restraints weight = 12663.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.139432 restraints weight = 8591.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.140889 restraints weight = 6462.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.6227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8934  Z= 0.185
  Angle     :  0.601   9.136  12080  Z= 0.316
  Chirality :  0.043   0.347   1410
  Planarity :  0.003   0.034   1472
  Dihedral  :  8.267 107.080   1198
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 23.30 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.25), residues: 1074
  helix:  1.92 (0.20), residues: 608
  sheet:  0.06 (0.53), residues: 100
  loop : -0.96 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 223 
 HIS   0.005   0.001   HIS D 244 
 PHE   0.041   0.002   PHE C 107 
 TYR   0.025   0.002   TYR C  99 
 ARG   0.004   0.000   ARG C 110 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2725.43 seconds
wall clock time: 49 minutes 52.56 seconds (2992.56 seconds total)