Starting phenix.real_space_refine
on Wed Feb 12 08:12:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xjh_22210/02_2025/6xjh_22210_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xjh_22210/02_2025/6xjh_22210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xjh_22210/02_2025/6xjh_22210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xjh_22210/02_2025/6xjh_22210.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xjh_22210/02_2025/6xjh_22210_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xjh_22210/02_2025/6xjh_22210_neut.cif"
  }
  resolution = 3.6
  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=   0.006
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      36      5.16       5
     C    5008      2.51       5
     N    1210      2.21       5
     O    1334      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7596
  Number of models: 1
  Model: ""
    Number of chains: 3
    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: 1736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1736
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
          Chain breaks: 1
    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}
  Restraints were copied for chains:
    D, B
  Time building chain proxies: 5.13, per 1000 atoms: 0.68
  Number of scatterers: 7596
  At special positions: 0
  Unit cell: (75.98, 100.87, 106.11, 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      36     16.00
     P       6     15.00
     Mg      2     11.99
     O    1334      8.00
     N    1210      7.00
     C    5008      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 998.0 milliseconds
  

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      67.3% alpha, 9.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  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 277 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 277 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 '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=AA4, 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: 7.460A  pdb=" N   LEU D 193 " --> pdb=" O   GLY D  30 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   ILE D  32 " --> pdb=" O   LEU D 193 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN D 200 " --> pdb=" O   PHE D 192 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ARG D 194 " --> pdb=" O   PHE D 198 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   PHE D 198 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)

    483 hydrogen bonds defined for protein.
    1389 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: 2.25

  Time building geometry restraints manager: 2.24 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: 1536
        1.32 -     1.47: 2716
        1.47 -     1.61: 3434
        1.61 -     1.75: 16
        1.75 -     1.90: 52
  Bond restraints: 7754
  Sorted by residual:
  bond pdb=" C   VAL D 199 "
       pdb=" N   GLN D 200 "
    ideal  model  delta    sigma   weight residual
    1.330  1.513 -0.183 1.45e-02 4.76e+03 1.59e+02
  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=" 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
  bond pdb=" CB  GLN B 222 "
       pdb=" CG  GLN B 222 "
    ideal  model  delta    sigma   weight residual
    1.520  1.360  0.160 3.00e-02 1.11e+03 2.83e+01
  ... (remaining 7749 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 9533
        2.66 -     5.32: 828
        5.32 -     7.98: 105
        7.98 -    10.65: 10
       10.65 -    13.31: 6
  Bond angle restraints: 10482
  Sorted by residual:
  angle pdb=" N   ILE B 167 "
        pdb=" CA  ILE B 167 "
        pdb=" C   ILE B 167 "
      ideal   model   delta    sigma   weight residual
     111.58  104.54    7.04 1.06e+00 8.90e-01 4.41e+01
  angle pdb=" N   ILE A 167 "
        pdb=" CA  ILE A 167 "
        pdb=" C   ILE A 167 "
      ideal   model   delta    sigma   weight residual
     111.58  104.55    7.03 1.06e+00 8.90e-01 4.40e+01
  angle pdb=" CA  PHE A  55 "
        pdb=" CB  PHE A  55 "
        pdb=" CG  PHE A  55 "
      ideal   model   delta    sigma   weight residual
     113.80  120.37   -6.57 1.00e+00 1.00e+00 4.32e+01
  angle pdb=" CA  PHE B  55 "
        pdb=" CB  PHE B  55 "
        pdb=" CG  PHE B  55 "
      ideal   model   delta    sigma   weight residual
     113.80  120.34   -6.54 1.00e+00 1.00e+00 4.28e+01
  angle pdb=" C   VAL B  -4 "
        pdb=" N   PRO B  -3 "
        pdb=" CA  PRO B  -3 "
      ideal   model   delta    sigma   weight residual
     119.56  126.19   -6.63 1.02e+00 9.61e-01 4.23e+01
  ... (remaining 10477 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.45: 4490
       22.45 -    44.89: 100
       44.89 -    67.34: 18
       67.34 -    89.78: 10
       89.78 -   112.23: 2
  Dihedral angle restraints: 4620
    sinusoidal: 1880
      harmonic: 2740
  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 4617 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 673
       0.067 -    0.134: 386
       0.134 -    0.201: 124
       0.201 -    0.268: 36
       0.268 -    0.335: 11
  Chirality restraints: 1230
  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  ARG D 189 "
            pdb=" N   ARG D 189 "
            pdb=" C   ARG D 189 "
            pdb=" CB  ARG D 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.60e+00
  ... (remaining 1227 not shown)

  Planarity restraints: 1264
  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  VAL C 199 "   -0.019 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   VAL C 199 "    0.061 2.00e-02 2.50e+03
        pdb=" O   VAL C 199 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   GLN C 200 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1261 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 799
        2.72 -     3.26: 8129
        3.26 -     3.81: 12766
        3.81 -     4.35: 16198
        4.35 -     4.90: 26334
  Nonbonded interactions: 64226
  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=" 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
  nonbonded pdb=" OG1 THR D  40 "
            pdb="MG    MG D 302 "
     model   vdw
     2.272 2.170
  ... (remaining 64221 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.230
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.750
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
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      :  0.019   0.183   7754  Z= 1.266
  Angle     :  1.641  13.306  10482  Z= 1.126
  Chirality :  0.095   0.335   1230
  Planarity :  0.008   0.036   1264
  Dihedral  : 11.428 112.230   2852
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  0.95 %
    Favored  : 98.57 %
  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 (0.26), residues: 928
  helix:  1.29 (0.20), residues: 558
  sheet:  1.10 (0.75), residues: 50
  loop : -0.22 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.007   TRP A 223 
 HIS   0.007   0.002   HIS C 178 
 PHE   0.030   0.006   PHE B  55 
 TYR   0.069   0.008   TYR B 206 
 ARG   0.011   0.002   ARG C 189 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  420 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 416
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 TYR cc_start: 0.8034 (t80) cc_final: 0.7750 (t80)
REVERT: A  115 HIS cc_start: 0.8383 (t-90) cc_final: 0.8132 (t-170)
REVERT: A  122 VAL cc_start: 0.8548 (t) cc_final: 0.7827 (t)
REVERT: A  130 ASN cc_start: 0.6500 (m-40) cc_final: 0.5964 (m-40)
REVERT: A  166 MET cc_start: 0.7154 (mmp) cc_final: 0.5945 (ptp)
REVERT: A  206 TYR cc_start: 0.7317 (p90) cc_final: 0.7025 (p90)
REVERT: A  209 ASP cc_start: 0.7685 (t70) cc_final: 0.7294 (m-30)
REVERT: A  220 ASN cc_start: 0.8146 (m-40) cc_final: 0.7893 (m110)
REVERT: A  223 TRP cc_start: 0.7890 (t-100) cc_final: 0.7351 (t60)
REVERT: A  243 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7856 (mmtt)
REVERT: B   42 MET cc_start: 0.4106 (tpt) cc_final: 0.3122 (ptt)
REVERT: B   70 VAL cc_start: 0.8394 (t) cc_final: 0.8048 (p)
REVERT: B  106 LEU cc_start: 0.8455 (mm) cc_final: 0.8242 (mt)
REVERT: B  115 HIS cc_start: 0.8191 (t-90) cc_final: 0.7622 (t-170)
REVERT: B  122 VAL cc_start: 0.8676 (t) cc_final: 0.8404 (t)
REVERT: B  209 ASP cc_start: 0.8031 (t70) cc_final: 0.7517 (m-30)
REVERT: B  211 MET cc_start: 0.8414 (mtp) cc_final: 0.8115 (mtm)
REVERT: B  220 ASN cc_start: 0.8351 (m-40) cc_final: 0.8095 (m110)
REVERT: B  221 TRP cc_start: 0.8291 (m100) cc_final: 0.7873 (m100)
REVERT: B  243 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8027 (mmtt)
REVERT: C    3 LEU cc_start: 0.8564 (mt) cc_final: 0.8234 (mt)
REVERT: C   43 MET cc_start: 0.8383 (mtm) cc_final: 0.8042 (mtp)
REVERT: C   49 ASN cc_start: 0.8163 (m110) cc_final: 0.7928 (m-40)
REVERT: C   56 LYS cc_start: 0.7501 (tttt) cc_final: 0.7300 (tptt)
REVERT: C   58 ASP cc_start: 0.7504 (t0) cc_final: 0.7233 (t70)
REVERT: C   63 ASP cc_start: 0.6664 (m-30) cc_final: 0.6409 (p0)
REVERT: C   71 HIS cc_start: 0.7468 (m-70) cc_final: 0.6291 (m-70)
REVERT: C   91 LEU cc_start: 0.8556 (mt) cc_final: 0.8300 (mp)
REVERT: C   99 TYR cc_start: 0.8282 (t80) cc_final: 0.7900 (t80)
REVERT: C  157 ASP cc_start: 0.8631 (m-30) cc_final: 0.8243 (t0)
REVERT: C  172 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7140 (mmm160)
REVERT: C  179 LYS cc_start: 0.8589 (mttt) cc_final: 0.8244 (mtpt)
REVERT: D   56 LYS cc_start: 0.7046 (tttt) cc_final: 0.6676 (tppt)
REVERT: D   58 ASP cc_start: 0.7536 (t0) cc_final: 0.7330 (m-30)
REVERT: D   75 TYR cc_start: 0.7969 (m-80) cc_final: 0.7756 (m-10)
REVERT: D   91 LEU cc_start: 0.8503 (mt) cc_final: 0.8190 (mp)
REVERT: D   99 TYR cc_start: 0.8610 (t80) cc_final: 0.8218 (t80)
REVERT: D  124 MET cc_start: 0.8329 (mtt) cc_final: 0.7843 (mtm)
REVERT: D  157 ASP cc_start: 0.8154 (m-30) cc_final: 0.7851 (t0)
REVERT: D  165 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mt)
REVERT: D  179 LYS cc_start: 0.8586 (mttt) cc_final: 0.8144 (mttp)
REVERT: D  183 ILE cc_start: 0.8217 (mt) cc_final: 0.7936 (mt)
REVERT: D  185 LEU cc_start: 0.8686 (tp) cc_final: 0.8457 (tt)
REVERT: D  194 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7549 (ttp80)
  outliers start: 4
  outliers final: 0
  residues processed: 416
  average time/residue: 0.2029
  time to fit residues: 111.6298
Evaluate side-chains
  237 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  44 ASN
** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 162 GLN
** C  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 126 GLN
C 178 HIS
C 200 GLN
** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D  47 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.093352 restraints weight = 13547.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.096886 restraints weight = 6791.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.099352 restraints weight = 4373.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7754  Z= 0.257
  Angle     :  0.707   7.424  10482  Z= 0.387
  Chirality :  0.047   0.196   1230
  Planarity :  0.004   0.033   1264
  Dihedral  : 10.228 120.937   1040
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 11.40 %
    Favored  : 84.20 %
  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:  1.97 (0.27), residues: 928
  helix:  2.29 (0.21), residues: 556
  sheet:  0.75 (0.69), residues: 58
  loop : -0.37 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 223 
 HIS   0.004   0.001   HIS B  47 
 PHE   0.019   0.002   PHE C  23 
 TYR   0.029   0.002   TYR B 206 
 ARG   0.005   0.001   ARG A  -2 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 287
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   34 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7350 (mm-40)
REVERT: A  130 ASN cc_start: 0.6491 (m-40) cc_final: 0.6250 (m110)
REVERT: A  141 TRP cc_start: 0.7846 (m100) cc_final: 0.7547 (m100)
REVERT: A  166 MET cc_start: 0.6543 (mmp) cc_final: 0.5521 (ttm)
REVERT: A  188 ILE cc_start: 0.6059 (mt) cc_final: 0.5852 (mm)
REVERT: A  204 PHE cc_start: 0.7330 (m-80) cc_final: 0.6329 (m-80)
REVERT: A  220 ASN cc_start: 0.8204 (m-40) cc_final: 0.7948 (m110)
REVERT: A  221 TRP cc_start: 0.8173 (m100) cc_final: 0.7958 (m100)
REVERT: A  233 PHE cc_start: 0.8222 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  243 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7797 (mmtt)
REVERT: B   -2 ARG cc_start: 0.6386 (mtm-85) cc_final: 0.6056 (mmm160)
REVERT: B   84 GLN cc_start: 0.8471 (tt0) cc_final: 0.7891 (tt0)
REVERT: B   87 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7244 (mmm)
REVERT: B  115 HIS cc_start: 0.7774 (t-90) cc_final: 0.7486 (t-170)
REVERT: B  122 VAL cc_start: 0.8641 (t) cc_final: 0.8165 (t)
REVERT: B  143 PHE cc_start: 0.8729 (m-80) cc_final: 0.8515 (m-80)
REVERT: B  152 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8653 (mm)
REVERT: B  243 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7870 (mmtt)
REVERT: C    2 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7354 (mtpp)
REVERT: C    4 GLU cc_start: 0.6851 (mp0) cc_final: 0.6497 (mp0)
REVERT: C   43 MET cc_start: 0.8010 (mtm) cc_final: 0.7782 (mtt)
REVERT: C   49 ASN cc_start: 0.8083 (m110) cc_final: 0.7850 (m-40)
REVERT: C   58 ASP cc_start: 0.6869 (t0) cc_final: 0.6564 (t70)
REVERT: C   70 GLU cc_start: 0.7627 (tp30) cc_final: 0.7295 (tp30)
REVERT: C   71 HIS cc_start: 0.7058 (m-70) cc_final: 0.6689 (m90)
REVERT: C   99 TYR cc_start: 0.8026 (t80) cc_final: 0.7538 (t80)
REVERT: C  172 ARG cc_start: 0.7246 (mmt-90) cc_final: 0.6945 (mmm160)
REVERT: C  181 GLU cc_start: 0.8364 (mp0) cc_final: 0.7970 (pm20)
REVERT: C  194 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7728 (ttp80)
REVERT: D    4 GLU cc_start: 0.7344 (mp0) cc_final: 0.6847 (mp0)
REVERT: D   64 ASN cc_start: 0.7583 (m-40) cc_final: 0.7287 (m110)
REVERT: D  165 LEU cc_start: 0.8757 (mt) cc_final: 0.8550 (mt)
REVERT: D  181 GLU cc_start: 0.8484 (mp0) cc_final: 0.7747 (pm20)
REVERT: D  185 LEU cc_start: 0.8594 (tp) cc_final: 0.8302 (tt)
REVERT: D  194 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.7590 (ttp80)
  outliers start: 37
  outliers final: 26
  residues processed: 314
  average time/residue: 0.1726
  time to fit residues: 74.6205
Evaluate side-chains
  260 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 231
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   35 SER
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue  100 THR
Chi-restraints excluded: chain C residue  105 ASP
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  197 HIS
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  176 SER
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  276 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0370
   chunk 51 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0010
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4064

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

Flipped N/Q/H residues before XYZ refinement:
B 162 GLN
B 220 ASN
** C  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN
** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D 285 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.093863 restraints weight = 13793.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.097443 restraints weight = 6806.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.099878 restraints weight = 4327.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.4488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7754  Z= 0.204
  Angle     :  0.625   7.801  10482  Z= 0.336
  Chirality :  0.045   0.187   1230
  Planarity :  0.004   0.035   1264
  Dihedral  :  9.921 114.357   1040
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 16.75 %
    Favored  : 78.86 %
  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:  1.51 (0.27), residues: 928
  helix:  2.06 (0.21), residues: 560
  sheet:  0.32 (0.70), residues: 58
  loop : -0.85 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  60 
 HIS   0.002   0.001   HIS C 197 
 PHE   0.023   0.002   PHE A 111 
 TYR   0.042   0.002   TYR A 206 
 ARG   0.002   0.000   ARG D 189 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 252
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.7107 (m-10) cc_final: 0.6160 (m-10)
REVERT: A  130 ASN cc_start: 0.6872 (m-40) cc_final: 0.6220 (m-40)
REVERT: A  141 TRP cc_start: 0.7750 (m100) cc_final: 0.7373 (m100)
REVERT: A  166 MET cc_start: 0.6195 (mmp) cc_final: 0.5257 (ttm)
REVERT: A  204 PHE cc_start: 0.7384 (m-80) cc_final: 0.6383 (m-80)
REVERT: A  220 ASN cc_start: 0.8249 (m-40) cc_final: 0.7978 (m110)
REVERT: A  221 TRP cc_start: 0.7921 (m100) cc_final: 0.7687 (m100)
REVERT: A  243 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7726 (mmtt)
REVERT: B   84 GLN cc_start: 0.8410 (tt0) cc_final: 0.8078 (tt0)
REVERT: B   87 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7032 (mmm)
REVERT: B  115 HIS cc_start: 0.7727 (t-90) cc_final: 0.7466 (t-170)
REVERT: B  152 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8663 (mm)
REVERT: B  243 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7881 (mmtt)
REVERT: C    2 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7285 (mtpp)
REVERT: C    3 LEU cc_start: 0.8743 (mt) cc_final: 0.8126 (mp)
REVERT: C    4 GLU cc_start: 0.6679 (mp0) cc_final: 0.6319 (mp0)
REVERT: C   43 MET cc_start: 0.7982 (mtm) cc_final: 0.7552 (mtt)
REVERT: C   71 HIS cc_start: 0.6984 (m-70) cc_final: 0.6629 (m90)
REVERT: C   99 TYR cc_start: 0.8063 (t80) cc_final: 0.7648 (t80)
REVERT: C  181 GLU cc_start: 0.8393 (mp0) cc_final: 0.7987 (pm20)
REVERT: C  200 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7247 (mt0)
REVERT: D    4 GLU cc_start: 0.7299 (mp0) cc_final: 0.6556 (mp0)
REVERT: D   64 ASN cc_start: 0.7574 (m-40) cc_final: 0.7273 (m110)
REVERT: D  105 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (m-30)
REVERT: D  165 LEU cc_start: 0.8563 (mt) cc_final: 0.8340 (mt)
REVERT: D  181 GLU cc_start: 0.8200 (mp0) cc_final: 0.7653 (pm20)
REVERT: D  185 LEU cc_start: 0.8676 (tp) cc_final: 0.8435 (tt)
REVERT: D  194 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.7548 (ttp80)
  outliers start: 37
  outliers final: 25
  residues processed: 274
  average time/residue: 0.1686
  time to fit residues: 64.1189
Evaluate side-chains
  252 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 222
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  191 TYR
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue  105 ASP
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0030
   chunk 38 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.1794

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 115 HIS
B 139 ASN
B 220 ASN
** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  71 HIS
D 285 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.112596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.092256 restraints weight = 14161.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.095601 restraints weight = 7223.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.097826 restraints weight = 4668.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.4846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7754  Z= 0.238
  Angle     :  0.613   7.249  10482  Z= 0.332
  Chirality :  0.045   0.354   1230
  Planarity :  0.004   0.035   1264
  Dihedral  :  9.787 111.728   1040
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 17.34 %
    Favored  : 76.96 %
  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:  1.25 (0.27), residues: 928
  helix:  1.85 (0.21), residues: 562
  sheet:  0.24 (0.72), residues: 58
  loop : -0.98 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  60 
 HIS   0.002   0.001   HIS D  71 
 PHE   0.033   0.002   PHE B 143 
 TYR   0.038   0.002   TYR A 206 
 ARG   0.007   0.001   ARG C 194 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 228
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7635 (mmtt)
REVERT: A  123 GLN cc_start: 0.8515 (tt0) cc_final: 0.7618 (mt0)
REVERT: A  130 ASN cc_start: 0.7068 (m-40) cc_final: 0.6288 (m-40)
REVERT: A  141 TRP cc_start: 0.7789 (m100) cc_final: 0.7411 (m100)
REVERT: A  166 MET cc_start: 0.6304 (mmp) cc_final: 0.5621 (ttm)
REVERT: A  204 PHE cc_start: 0.7543 (m-80) cc_final: 0.6495 (m-80)
REVERT: A  220 ASN cc_start: 0.8111 (m-40) cc_final: 0.7870 (m110)
REVERT: A  221 TRP cc_start: 0.7875 (m100) cc_final: 0.7590 (m100)
REVERT: A  233 PHE cc_start: 0.8242 (m-80) cc_final: 0.7899 (m-80)
REVERT: A  243 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7715 (mmtt)
REVERT: B   11 LEU cc_start: 0.8139 (mt) cc_final: 0.7880 (tt)
REVERT: B   51 TYR cc_start: 0.6895 (m-10) cc_final: 0.6613 (m-80)
REVERT: B   84 GLN cc_start: 0.8394 (tt0) cc_final: 0.7979 (tp40)
REVERT: B   87 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7132 (mmm)
REVERT: B  139 ASN cc_start: 0.8236 (t0) cc_final: 0.7571 (t0)
REVERT: B  152 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8746 (mm)
REVERT: B  188 ILE cc_start: 0.6043 (mm) cc_final: 0.5716 (mt)
REVERT: B  200 ASP cc_start: 0.8200 (m-30) cc_final: 0.7860 (t0)
REVERT: B  243 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7918 (mmtt)
REVERT: C    2 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7301 (mtpp)
REVERT: C    4 GLU cc_start: 0.6857 (mp0) cc_final: 0.6439 (mp0)
REVERT: C   43 MET cc_start: 0.8014 (mtm) cc_final: 0.7675 (mtt)
REVERT: C   71 HIS cc_start: 0.6952 (m-70) cc_final: 0.6611 (m90)
REVERT: C   99 TYR cc_start: 0.8027 (t80) cc_final: 0.7610 (t80)
REVERT: C  144 ASP cc_start: 0.8125 (t0) cc_final: 0.7534 (t0)
REVERT: C  181 GLU cc_start: 0.8381 (mp0) cc_final: 0.8109 (pm20)
REVERT: D    3 LEU cc_start: 0.8927 (mt) cc_final: 0.8683 (mt)
REVERT: D    4 GLU cc_start: 0.7357 (mp0) cc_final: 0.7014 (mp0)
REVERT: D   43 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.8050 (mtt)
REVERT: D   64 ASN cc_start: 0.7784 (m-40) cc_final: 0.7424 (m110)
REVERT: D  105 ASP cc_start: 0.7881 (m-30) cc_final: 0.7648 (m-30)
REVERT: D  194 ARG cc_start: 0.7802 (ttp-170) cc_final: 0.7417 (ttp80)
REVERT: D  285 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7245 (t0)
  outliers start: 48
  outliers final: 34
  residues processed: 255
  average time/residue: 0.1754
  time to fit residues: 62.4108
Evaluate side-chains
  254 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 215
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   43 MET
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  276 SER
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0040
   overall best weight:    1.3798

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 GLN
C 200 GLN
** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D  71 HIS
D 285 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.111558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.091251 restraints weight = 14137.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.094515 restraints weight = 7158.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.096560 restraints weight = 4616.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.5075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7754  Z= 0.247
  Angle     :  0.618   7.066  10482  Z= 0.329
  Chirality :  0.045   0.334   1230
  Planarity :  0.004   0.034   1264
  Dihedral  :  9.633 107.035   1040
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  7.13 %
    Allowed  : 17.10 %
    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:  1.14 (0.27), residues: 928
  helix:  1.77 (0.21), residues: 564
  sheet:  0.04 (0.71), residues: 58
  loop : -1.04 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 223 
 HIS   0.002   0.001   HIS D  71 
 PHE   0.019   0.001   PHE A 111 
 TYR   0.042   0.002   TYR A 206 
 ARG   0.002   0.000   ARG B 190 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 222
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7616 (mmtt)
REVERT: A   51 TYR cc_start: 0.7219 (m-10) cc_final: 0.6908 (m-10)
REVERT: A  123 GLN cc_start: 0.8628 (tt0) cc_final: 0.7898 (tp40)
REVERT: A  130 ASN cc_start: 0.7179 (m-40) cc_final: 0.6167 (m-40)
REVERT: A  141 TRP cc_start: 0.7794 (m100) cc_final: 0.7410 (m100)
REVERT: A  166 MET cc_start: 0.6131 (mmp) cc_final: 0.5506 (ttm)
REVERT: A  220 ASN cc_start: 0.8198 (m-40) cc_final: 0.7960 (m110)
REVERT: A  221 TRP cc_start: 0.7903 (m100) cc_final: 0.7665 (m100)
REVERT: A  233 PHE cc_start: 0.8228 (m-80) cc_final: 0.7850 (m-80)
REVERT: B   11 LEU cc_start: 0.8053 (mt) cc_final: 0.7811 (tt)
REVERT: B   51 TYR cc_start: 0.7047 (m-10) cc_final: 0.6843 (m-80)
REVERT: B   84 GLN cc_start: 0.8439 (tt0) cc_final: 0.8013 (tp40)
REVERT: B   87 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7450 (mmm)
REVERT: B  152 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8706 (mm)
REVERT: B  166 MET cc_start: 0.5432 (mmt) cc_final: 0.4647 (ttm)
REVERT: B  188 ILE cc_start: 0.6094 (mm) cc_final: 0.5746 (mt)
REVERT: B  200 ASP cc_start: 0.8272 (m-30) cc_final: 0.7724 (t0)
REVERT: B  243 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7950 (mmtt)
REVERT: B  245 ASP cc_start: 0.5244 (m-30) cc_final: 0.5004 (m-30)
REVERT: C    2 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7286 (mtpp)
REVERT: C   43 MET cc_start: 0.8074 (mtm) cc_final: 0.7835 (mtt)
REVERT: C   70 GLU cc_start: 0.7684 (tp30) cc_final: 0.7179 (tp30)
REVERT: C   71 HIS cc_start: 0.6946 (m-70) cc_final: 0.6618 (m90)
REVERT: C   99 TYR cc_start: 0.8122 (t80) cc_final: 0.7774 (t80)
REVERT: C  181 GLU cc_start: 0.8499 (mp0) cc_final: 0.8143 (pm20)
REVERT: C  200 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6986 (mt0)
REVERT: C  202 VAL cc_start: 0.7672 (t) cc_final: 0.7353 (m)
REVERT: C  204 MET cc_start: 0.6464 (pmm) cc_final: 0.6217 (pmm)
REVERT: D    4 GLU cc_start: 0.7349 (mp0) cc_final: 0.6962 (mp0)
REVERT: D  124 MET cc_start: 0.8317 (mtm) cc_final: 0.7712 (mtm)
REVERT: D  194 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7426 (ttp80)
REVERT: D  285 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.6995 (t0)
  outliers start: 60
  outliers final: 39
  residues processed: 256
  average time/residue: 0.1618
  time to fit residues: 58.2784
Evaluate side-chains
  254 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 210
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   87 MET
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  197 HIS
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  150 MET
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  276 SER
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 66 optimal weight:    0.3980
   chunk 43 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 56 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 285 ASN
D  35 ASN
D  71 HIS
D 285 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.112979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.092831 restraints weight = 13980.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.096066 restraints weight = 7232.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.098292 restraints weight = 4721.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.5261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7754  Z= 0.190
  Angle     :  0.601   7.540  10482  Z= 0.319
  Chirality :  0.044   0.284   1230
  Planarity :  0.003   0.034   1264
  Dihedral  :  9.447 104.366   1040
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 18.88 %
    Favored  : 75.42 %
  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:  1.11 (0.27), residues: 928
  helix:  1.72 (0.21), residues: 570
  sheet:  0.07 (0.71), residues: 58
  loop : -1.03 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.002   0.000   HIS D  71 
 PHE   0.018   0.001   PHE A 111 
 TYR   0.045   0.001   TYR A 206 
 ARG   0.002   0.000   ARG C 189 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 231
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7674 (mmtt)
REVERT: A   51 TYR cc_start: 0.7187 (m-10) cc_final: 0.6925 (m-10)
REVERT: A  123 GLN cc_start: 0.8509 (tt0) cc_final: 0.8196 (tp40)
REVERT: A  130 ASN cc_start: 0.7212 (m-40) cc_final: 0.6579 (m-40)
REVERT: A  141 TRP cc_start: 0.7808 (m100) cc_final: 0.7441 (m100)
REVERT: A  166 MET cc_start: 0.5909 (mmp) cc_final: 0.5308 (ttm)
REVERT: A  204 PHE cc_start: 0.7390 (m-80) cc_final: 0.6265 (m-80)
REVERT: A  220 ASN cc_start: 0.8038 (m-40) cc_final: 0.7827 (m110)
REVERT: A  221 TRP cc_start: 0.7839 (m100) cc_final: 0.7596 (m100)
REVERT: A  233 PHE cc_start: 0.8315 (m-80) cc_final: 0.7957 (m-80)
REVERT: B   11 LEU cc_start: 0.8076 (mt) cc_final: 0.7562 (tt)
REVERT: B   15 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7193 (m-10)
REVERT: B   60 TRP cc_start: 0.8354 (t60) cc_final: 0.8141 (t60)
REVERT: B   84 GLN cc_start: 0.8341 (tt0) cc_final: 0.8030 (tp40)
REVERT: B  152 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: B  166 MET cc_start: 0.5445 (mmt) cc_final: 0.4755 (ttm)
REVERT: B  188 ILE cc_start: 0.5956 (mm) cc_final: 0.5660 (mt)
REVERT: B  200 ASP cc_start: 0.8106 (m-30) cc_final: 0.7716 (t0)
REVERT: B  243 LYS cc_start: 0.8331 (mmtt) cc_final: 0.7969 (mmtt)
REVERT: B  245 ASP cc_start: 0.5422 (m-30) cc_final: 0.5167 (m-30)
REVERT: C    1 MET cc_start: 0.6845 (tpp) cc_final: 0.6606 (tpt)
REVERT: C    2 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7252 (mtpp)
REVERT: C    4 GLU cc_start: 0.7248 (mp0) cc_final: 0.6805 (mp0)
REVERT: C   99 TYR cc_start: 0.8114 (t80) cc_final: 0.7845 (t80)
REVERT: C  181 GLU cc_start: 0.8523 (mp0) cc_final: 0.8213 (pm20)
REVERT: C  194 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7516 (ttp80)
REVERT: C  202 VAL cc_start: 0.7678 (t) cc_final: 0.7274 (m)
REVERT: D    4 GLU cc_start: 0.7336 (mp0) cc_final: 0.6982 (mp0)
REVERT: D  124 MET cc_start: 0.8260 (mtm) cc_final: 0.7737 (mtm)
REVERT: D  194 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7397 (ttp80)
REVERT: D  285 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.6911 (t0)
  outliers start: 48
  outliers final: 33
  residues processed: 257
  average time/residue: 0.1652
  time to fit residues: 59.3459
Evaluate side-chains
  254 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 217
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   15 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  150 MET
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0870
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D  71 HIS
D 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.113256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.093081 restraints weight = 14014.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.096391 restraints weight = 7091.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.098661 restraints weight = 4556.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7754  Z= 0.197
  Angle     :  0.610   8.348  10482  Z= 0.320
  Chirality :  0.044   0.236   1230
  Planarity :  0.003   0.033   1264
  Dihedral  :  9.329 102.340   1040
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 20.07 %
    Favored  : 74.23 %
  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 (0.27), residues: 928
  helix:  1.74 (0.21), residues: 570
  sheet: -0.07 (0.70), residues: 58
  loop : -1.11 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 223 
 HIS   0.005   0.001   HIS C  71 
 PHE   0.017   0.001   PHE A 111 
 TYR   0.046   0.001   TYR A 206 
 ARG   0.002   0.000   ARG D 278 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 224
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7658 (mmtt)
REVERT: A   31 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8817 (mp)
REVERT: A   34 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7718 (mp10)
REVERT: A   51 TYR cc_start: 0.7245 (m-10) cc_final: 0.6944 (m-10)
REVERT: A  123 GLN cc_start: 0.8571 (tt0) cc_final: 0.8221 (tp40)
REVERT: A  130 ASN cc_start: 0.7315 (m-40) cc_final: 0.6719 (m-40)
REVERT: A  141 TRP cc_start: 0.7818 (m100) cc_final: 0.7433 (m100)
REVERT: A  166 MET cc_start: 0.5875 (mmp) cc_final: 0.5181 (ttm)
REVERT: A  204 PHE cc_start: 0.7510 (m-80) cc_final: 0.6340 (m-80)
REVERT: A  221 TRP cc_start: 0.7853 (m100) cc_final: 0.7621 (m100)
REVERT: A  233 PHE cc_start: 0.8237 (m-80) cc_final: 0.7905 (m-80)
REVERT: B   15 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.7221 (m-10)
REVERT: B   84 GLN cc_start: 0.8414 (tt0) cc_final: 0.8025 (tp40)
REVERT: B   87 MET cc_start: 0.8182 (mmm) cc_final: 0.7788 (mmm)
REVERT: B  115 HIS cc_start: 0.7671 (t-170) cc_final: 0.7411 (t-170)
REVERT: B  152 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8659 (mm)
REVERT: B  166 MET cc_start: 0.5376 (mmt) cc_final: 0.4634 (ttm)
REVERT: B  188 ILE cc_start: 0.5929 (mm) cc_final: 0.5722 (mt)
REVERT: B  200 ASP cc_start: 0.8146 (m-30) cc_final: 0.7671 (t0)
REVERT: B  243 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7968 (mmtt)
REVERT: B  245 ASP cc_start: 0.5638 (m-30) cc_final: 0.5366 (m-30)
REVERT: C    2 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7216 (mtpp)
REVERT: C    4 GLU cc_start: 0.7131 (mp0) cc_final: 0.6580 (mp0)
REVERT: C   70 GLU cc_start: 0.7649 (tp30) cc_final: 0.7336 (tp30)
REVERT: C   99 TYR cc_start: 0.8152 (t80) cc_final: 0.7771 (t80)
REVERT: C  181 GLU cc_start: 0.8526 (mp0) cc_final: 0.8181 (pm20)
REVERT: C  194 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7405 (ttp80)
REVERT: C  204 MET cc_start: 0.6854 (pmm) cc_final: 0.6526 (pmm)
REVERT: D    4 GLU cc_start: 0.7315 (mp0) cc_final: 0.6923 (mp0)
REVERT: D  124 MET cc_start: 0.8255 (mtm) cc_final: 0.7657 (mtm)
REVERT: D  194 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7400 (ttp80)
REVERT: D  204 MET cc_start: 0.6947 (pmm) cc_final: 0.6694 (pmm)
REVERT: D  285 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.6622 (t0)
  outliers start: 48
  outliers final: 35
  residues processed: 248
  average time/residue: 0.1609
  time to fit residues: 55.7161
Evaluate side-chains
  252 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 212
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   15 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  190 ARG
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  150 MET
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 ASN
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D  71 HIS
D 285 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.091634 restraints weight = 14299.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.094878 restraints weight = 7175.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.097159 restraints weight = 4629.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.5591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7754  Z= 0.200
  Angle     :  0.624  11.991  10482  Z= 0.327
  Chirality :  0.044   0.216   1230
  Planarity :  0.003   0.034   1264
  Dihedral  :  9.192 100.132   1040
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 19.95 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.27), residues: 928
  helix:  1.65 (0.21), residues: 570
  sheet: -0.13 (0.70), residues: 58
  loop : -1.22 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  60 
 HIS   0.004   0.001   HIS C  71 
 PHE   0.017   0.001   PHE A 111 
 TYR   0.045   0.001   TYR A 206 
 ARG   0.002   0.000   ARG D 287 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 216
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7633 (mmtt)
REVERT: A   31 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8800 (mp)
REVERT: A   51 TYR cc_start: 0.7248 (m-10) cc_final: 0.6968 (m-10)
REVERT: A  123 GLN cc_start: 0.8584 (tt0) cc_final: 0.8351 (tp40)
REVERT: A  130 ASN cc_start: 0.7398 (m-40) cc_final: 0.7031 (m110)
REVERT: A  141 TRP cc_start: 0.7778 (m100) cc_final: 0.7436 (m100)
REVERT: A  166 MET cc_start: 0.5838 (mmp) cc_final: 0.5147 (ttm)
REVERT: A  204 PHE cc_start: 0.7392 (m-80) cc_final: 0.6219 (m-80)
REVERT: A  221 TRP cc_start: 0.7858 (m100) cc_final: 0.7628 (m100)
REVERT: B   12 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6856 (m-80)
REVERT: B   15 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7224 (m-10)
REVERT: B   84 GLN cc_start: 0.8430 (tt0) cc_final: 0.8079 (tp40)
REVERT: B  115 HIS cc_start: 0.7679 (t-170) cc_final: 0.7452 (t-170)
REVERT: B  152 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8729 (mm)
REVERT: B  166 MET cc_start: 0.5326 (mmt) cc_final: 0.4510 (ttm)
REVERT: B  188 ILE cc_start: 0.6016 (mm) cc_final: 0.5711 (mt)
REVERT: B  243 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7962 (mmtt)
REVERT: B  245 ASP cc_start: 0.5738 (m-30) cc_final: 0.5533 (m-30)
REVERT: C    1 MET cc_start: 0.6554 (tpp) cc_final: 0.6213 (tpt)
REVERT: C    4 GLU cc_start: 0.7114 (mp0) cc_final: 0.6530 (mp0)
REVERT: C   70 GLU cc_start: 0.7690 (tp30) cc_final: 0.7365 (tp30)
REVERT: C   99 TYR cc_start: 0.8179 (t80) cc_final: 0.7886 (t80)
REVERT: C  181 GLU cc_start: 0.8524 (mp0) cc_final: 0.8188 (pm20)
REVERT: C  194 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7394 (ttp80)
REVERT: D    4 GLU cc_start: 0.7328 (mp0) cc_final: 0.6923 (mp0)
REVERT: D  124 MET cc_start: 0.8253 (mtm) cc_final: 0.7636 (mtm)
REVERT: D  194 ARG cc_start: 0.7957 (ttp-170) cc_final: 0.7412 (ttp80)
REVERT: D  285 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.6509 (t0)
  outliers start: 47
  outliers final: 39
  residues processed: 244
  average time/residue: 0.1764
  time to fit residues: 60.2509
Evaluate side-chains
  255 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 211
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   12 TYR
Chi-restraints excluded: chain B residue   15 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  197 HIS
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  150 MET
Chi-restraints excluded: chain D residue  155 SER
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 ASN
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 126 GLN
C 200 GLN
D  35 ASN
D  71 HIS
D 285 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.111850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.091396 restraints weight = 14364.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.094698 restraints weight = 7224.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.096798 restraints weight = 4643.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.5689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7754  Z= 0.200
  Angle     :  0.627   9.424  10482  Z= 0.330
  Chirality :  0.044   0.194   1230
  Planarity :  0.003   0.034   1264
  Dihedral  :  9.079  99.524   1040
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 20.67 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.27), residues: 928
  helix:  1.65 (0.21), residues: 570
  sheet: -0.16 (0.71), residues: 58
  loop : -1.30 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  60 
 HIS   0.004   0.001   HIS C  71 
 PHE   0.035   0.001   PHE B 218 
 TYR   0.047   0.001   TYR A 206 
 ARG   0.002   0.000   ARG D 287 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 212
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7657 (mmtt)
REVERT: A   31 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8789 (mp)
REVERT: A   51 TYR cc_start: 0.7255 (m-10) cc_final: 0.6943 (m-10)
REVERT: A  123 GLN cc_start: 0.8589 (tt0) cc_final: 0.8355 (tp40)
REVERT: A  130 ASN cc_start: 0.7137 (m-40) cc_final: 0.6740 (m110)
REVERT: A  141 TRP cc_start: 0.7768 (m100) cc_final: 0.7434 (m100)
REVERT: A  166 MET cc_start: 0.5814 (mmp) cc_final: 0.5161 (ttm)
REVERT: A  204 PHE cc_start: 0.7597 (m-80) cc_final: 0.6413 (m-80)
REVERT: A  221 TRP cc_start: 0.7852 (m100) cc_final: 0.7626 (m100)
REVERT: A  233 PHE cc_start: 0.8035 (m-80) cc_final: 0.7717 (m-80)
REVERT: B   15 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7248 (m-10)
REVERT: B   84 GLN cc_start: 0.8427 (tt0) cc_final: 0.8071 (tp40)
REVERT: B  115 HIS cc_start: 0.7699 (t-170) cc_final: 0.7485 (t-170)
REVERT: B  152 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: B  166 MET cc_start: 0.5354 (mmt) cc_final: 0.4426 (ttm)
REVERT: B  188 ILE cc_start: 0.6028 (mm) cc_final: 0.5720 (mt)
REVERT: B  200 ASP cc_start: 0.8211 (m-30) cc_final: 0.7731 (t0)
REVERT: B  243 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7941 (mmtt)
REVERT: B  245 ASP cc_start: 0.5830 (m-30) cc_final: 0.5601 (m-30)
REVERT: C    4 GLU cc_start: 0.7112 (mp0) cc_final: 0.6607 (mp0)
REVERT: C   70 GLU cc_start: 0.7678 (tp30) cc_final: 0.7393 (tp30)
REVERT: C   99 TYR cc_start: 0.8174 (t80) cc_final: 0.7936 (t80)
REVERT: C  181 GLU cc_start: 0.8469 (mp0) cc_final: 0.8189 (pm20)
REVERT: C  194 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7369 (ttp80)
REVERT: C  200 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6942 (mt0)
REVERT: C  285 ASN cc_start: 0.7453 (t0) cc_final: 0.6927 (t0)
REVERT: D    4 GLU cc_start: 0.7335 (mp0) cc_final: 0.6926 (mp0)
REVERT: D  124 MET cc_start: 0.8258 (mtm) cc_final: 0.7631 (mtm)
REVERT: D  194 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7466 (ttp80)
REVERT: D  285 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.6408 (t0)
  outliers start: 44
  outliers final: 36
  residues processed: 238
  average time/residue: 0.1633
  time to fit residues: 54.1202
Evaluate side-chains
  250 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 209
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   15 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  223 TRP
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  197 HIS
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  150 MET
Chi-restraints excluded: chain D residue  155 SER
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0970
   chunk 54 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.091401 restraints weight = 14327.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.094703 restraints weight = 7242.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.096979 restraints weight = 4667.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.5794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   7754  Z= 0.193
  Angle     :  0.621   9.131  10482  Z= 0.328
  Chirality :  0.043   0.186   1230
  Planarity :  0.003   0.035   1264
  Dihedral  :  8.989  98.197   1040
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 21.26 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.27), residues: 928
  helix:  1.67 (0.21), residues: 570
  sheet: -0.25 (0.72), residues: 58
  loop : -1.37 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  60 
 HIS   0.003   0.001   HIS C  71 
 PHE   0.033   0.001   PHE B 218 
 TYR   0.045   0.002   TYR A 206 
 ARG   0.002   0.000   ARG D 287 

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

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

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1856 Ramachandran restraints generated.
    928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 218
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8829 (mp)
REVERT: A   51 TYR cc_start: 0.7244 (m-10) cc_final: 0.7017 (m-10)
REVERT: A  123 GLN cc_start: 0.8587 (tt0) cc_final: 0.7698 (tp40)
REVERT: A  130 ASN cc_start: 0.7161 (m-40) cc_final: 0.5839 (m-40)
REVERT: A  141 TRP cc_start: 0.7775 (m100) cc_final: 0.7446 (m100)
REVERT: A  166 MET cc_start: 0.6059 (mmp) cc_final: 0.5217 (ttm)
REVERT: A  204 PHE cc_start: 0.7617 (m-80) cc_final: 0.6459 (m-80)
REVERT: A  221 TRP cc_start: 0.7850 (m100) cc_final: 0.7635 (m100)
REVERT: B   15 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7278 (m-10)
REVERT: B   84 GLN cc_start: 0.8409 (tt0) cc_final: 0.8075 (tp40)
REVERT: B  115 HIS cc_start: 0.7706 (t-170) cc_final: 0.7498 (t-170)
REVERT: B  152 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8726 (mm)
REVERT: B  166 MET cc_start: 0.5342 (mmt) cc_final: 0.4456 (ttm)
REVERT: B  188 ILE cc_start: 0.6005 (mm) cc_final: 0.5705 (mt)
REVERT: B  243 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7934 (mmtt)
REVERT: C    4 GLU cc_start: 0.7137 (mp0) cc_final: 0.6632 (mp0)
REVERT: C   70 GLU cc_start: 0.7638 (tp30) cc_final: 0.7430 (tp30)
REVERT: C  181 GLU cc_start: 0.8426 (mp0) cc_final: 0.8153 (pm20)
REVERT: C  194 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7358 (ttp80)
REVERT: C  285 ASN cc_start: 0.7497 (t0) cc_final: 0.6922 (t0)
REVERT: D   70 GLU cc_start: 0.7224 (tp30) cc_final: 0.6812 (tp30)
REVERT: D  124 MET cc_start: 0.8207 (mtm) cc_final: 0.7638 (mtm)
REVERT: D  194 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7531 (ttp80)
REVERT: D  285 ASN cc_start: 0.6806 (OUTLIER) cc_final: 0.5885 (t0)
  outliers start: 43
  outliers final: 36
  residues processed: 244
  average time/residue: 0.1672
  time to fit residues: 56.9045
Evaluate side-chains
  251 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 211
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   73 THR
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  127 ASN
Chi-restraints excluded: chain A residue  143 PHE
Chi-restraints excluded: chain A residue  162 GLN
Chi-restraints excluded: chain A residue  226 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   15 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain C residue    2 LYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  164 SER
Chi-restraints excluded: chain C residue  276 SER
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   35 ASN
Chi-restraints excluded: chain D residue   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  109 MET
Chi-restraints excluded: chain D residue  150 MET
Chi-restraints excluded: chain D residue  155 SER
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  276 SER
Chi-restraints excluded: chain D residue  285 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0970
   chunk 25 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  35 ASN
D 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.110434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.089836 restraints weight = 14152.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.093013 restraints weight = 7290.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.095256 restraints weight = 4768.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.5869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   7754  Z= 0.263
  Angle     :  0.660   9.362  10482  Z= 0.347
  Chirality :  0.045   0.264   1230
  Planarity :  0.004   0.036   1264
  Dihedral  :  9.010  97.774   1040
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 21.14 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 928
  helix:  1.64 (0.21), residues: 570
  sheet: -0.37 (0.70), residues: 58
  loop : -1.40 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  60 
 HIS   0.004   0.001   HIS D  71 
 PHE   0.029   0.002   PHE B 218 
 TYR   0.043   0.002   TYR A 206 
 ARG   0.003   0.001   ARG D 189 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2391.14 seconds
wall clock time: 43 minutes 47.16 seconds (2627.16 seconds total)