Starting phenix.real_space_refine
on Fri Jul 25 12:06:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xjh_22210/07_2025/6xjh_22210_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xjh_22210/07_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_22210/07_2025/6xjh_22210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xjh_22210/07_2025/6xjh_22210.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xjh_22210/07_2025/6xjh_22210_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xjh_22210/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.49, per 1000 atoms: 0.72
  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: 2.09
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.87
  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: 2.45

  Time building geometry restraints manager: 2.43 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: 0.04
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:                    0.080
  Process input model:                     22.020
  Find NCS groups from input model:        0.130
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.740
-------------------------------------------------------------------------------
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= 1.071
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15736 (  483)
  hydrogen bonds       : angle       6.87876 ( 1389)
  covalent geometry    : bond        0.01931 ( 7754)
  covalent geometry    : angle       1.64065 (10482)

*********************** 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  : 0.888 
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: 0.1953
  time to fit residues: 107.5479
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  : 0.913 
-------------------------------------------------------------------------------
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 = 35)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.093299 restraints weight = 13547.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.096900 restraints weight = 6814.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.099359 restraints weight = 4372.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
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= 0.188
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06275 (  483)
  hydrogen bonds       : angle       5.04871 ( 1389)
  covalent geometry    : bond        0.00407 ( 7754)
  covalent geometry    : angle       0.70744 (10482)

*********************** 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  : 0.894 
Fit side-chains
REVERT: A   34 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7330 (mm-40)
REVERT: A  130 ASN cc_start: 0.6469 (m-40) cc_final: 0.6221 (m110)
REVERT: A  141 TRP cc_start: 0.7851 (m100) cc_final: 0.7551 (m100)
REVERT: A  166 MET cc_start: 0.6556 (mmp) cc_final: 0.5561 (ttm)
REVERT: A  188 ILE cc_start: 0.6072 (mt) cc_final: 0.5853 (mm)
REVERT: A  204 PHE cc_start: 0.7344 (m-80) cc_final: 0.6354 (m-80)
REVERT: A  220 ASN cc_start: 0.8175 (m-40) cc_final: 0.7915 (m110)
REVERT: A  221 TRP cc_start: 0.8158 (m100) cc_final: 0.7940 (m100)
REVERT: A  233 PHE cc_start: 0.8239 (m-80) cc_final: 0.7956 (m-80)
REVERT: A  243 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7801 (mmtt)
REVERT: B   -2 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.6065 (mmm160)
REVERT: B   84 GLN cc_start: 0.8453 (tt0) cc_final: 0.7892 (tt0)
REVERT: B   87 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7224 (mmm)
REVERT: B  115 HIS cc_start: 0.7785 (t-90) cc_final: 0.7500 (t-170)
REVERT: B  122 VAL cc_start: 0.8670 (t) cc_final: 0.8193 (t)
REVERT: B  143 PHE cc_start: 0.8733 (m-80) cc_final: 0.8518 (m-80)
REVERT: B  152 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (mm)
REVERT: B  243 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7878 (mmtt)
REVERT: C    2 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7384 (mtpp)
REVERT: C    4 GLU cc_start: 0.6888 (mp0) cc_final: 0.6541 (mp0)
REVERT: C   43 MET cc_start: 0.7973 (mtm) cc_final: 0.7758 (mtt)
REVERT: C   49 ASN cc_start: 0.8076 (m110) cc_final: 0.7853 (m-40)
REVERT: C   58 ASP cc_start: 0.6840 (t0) cc_final: 0.6531 (t70)
REVERT: C   70 GLU cc_start: 0.7616 (tp30) cc_final: 0.7288 (tp30)
REVERT: C   71 HIS cc_start: 0.7052 (m-70) cc_final: 0.6687 (m90)
REVERT: C   99 TYR cc_start: 0.8013 (t80) cc_final: 0.7542 (t80)
REVERT: C  172 ARG cc_start: 0.7265 (mmt-90) cc_final: 0.6965 (mmm160)
REVERT: C  181 GLU cc_start: 0.8349 (mp0) cc_final: 0.7965 (pm20)
REVERT: C  194 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7753 (ttp80)
REVERT: D    4 GLU cc_start: 0.7362 (mp0) cc_final: 0.6855 (mp0)
REVERT: D   64 ASN cc_start: 0.7587 (m-40) cc_final: 0.7298 (m110)
REVERT: D  165 LEU cc_start: 0.8732 (mt) cc_final: 0.8530 (mt)
REVERT: D  181 GLU cc_start: 0.8460 (mp0) cc_final: 0.7732 (pm20)
REVERT: D  185 LEU cc_start: 0.8577 (tp) cc_final: 0.8286 (tt)
REVERT: D  194 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.7593 (ttp80)
  outliers start: 37
  outliers final: 26
  residues processed: 314
  average time/residue: 0.1653
  time to fit residues: 71.6133
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  : 0.878 
-------------------------------------------------------------------------------
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:    0.0030
   chunk 51 optimal weight:    0.6980
   chunk 79 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0010
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.114730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.093964 restraints weight = 13808.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.097509 restraints weight = 6798.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.099954 restraints weight = 4329.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7754  Z= 0.147
  Angle     :  0.621   7.834  10482  Z= 0.335
  Chirality :  0.045   0.188   1230
  Planarity :  0.004   0.035   1264
  Dihedral  :  9.915 113.934   1040
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 12.05
  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:  0.30 (0.70), residues: 58
  loop : -0.85 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  60 
 HIS   0.002   0.001   HIS C 197 
 PHE   0.023   0.002   PHE A 111 
 TYR   0.044   0.002   TYR A 206 
 ARG   0.002   0.000   ARG D 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05228 (  483)
  hydrogen bonds       : angle       4.83338 ( 1389)
  covalent geometry    : bond        0.00303 ( 7754)
  covalent geometry    : angle       0.62110 (10482)

*********************** 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
  288 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 251
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A  130 ASN cc_start: 0.6807 (m-40) cc_final: 0.5873 (m-40)
REVERT: A  141 TRP cc_start: 0.7751 (m100) cc_final: 0.7372 (m100)
REVERT: A  166 MET cc_start: 0.6194 (mmp) cc_final: 0.5256 (ttm)
REVERT: A  204 PHE cc_start: 0.7387 (m-80) cc_final: 0.6384 (m-80)
REVERT: A  220 ASN cc_start: 0.8251 (m-40) cc_final: 0.7979 (m110)
REVERT: A  221 TRP cc_start: 0.7920 (m100) cc_final: 0.7687 (m100)
REVERT: A  243 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7728 (mmtt)
REVERT: B   84 GLN cc_start: 0.8410 (tt0) cc_final: 0.8079 (tt0)
REVERT: B   87 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7033 (mmm)
REVERT: B  115 HIS cc_start: 0.7728 (t-90) cc_final: 0.7466 (t-170)
REVERT: B  152 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8664 (mm)
REVERT: B  243 LYS cc_start: 0.8402 (mmtt) cc_final: 0.7883 (mmtt)
REVERT: C    2 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7286 (mtpp)
REVERT: C    3 LEU cc_start: 0.8742 (mt) cc_final: 0.8129 (mp)
REVERT: C    4 GLU cc_start: 0.6681 (mp0) cc_final: 0.6320 (mp0)
REVERT: C   43 MET cc_start: 0.7981 (mtm) cc_final: 0.7551 (mtt)
REVERT: C   71 HIS cc_start: 0.7023 (m-70) cc_final: 0.6665 (m90)
REVERT: C   99 TYR cc_start: 0.8064 (t80) cc_final: 0.7649 (t80)
REVERT: C  181 GLU cc_start: 0.8391 (mp0) cc_final: 0.7986 (pm20)
REVERT: C  200 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7078 (mt0)
REVERT: D    4 GLU cc_start: 0.7305 (mp0) cc_final: 0.6558 (mp0)
REVERT: D   64 ASN cc_start: 0.7575 (m-40) cc_final: 0.7274 (m110)
REVERT: D  105 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7728 (m-30)
REVERT: D  124 MET cc_start: 0.8383 (mtm) cc_final: 0.8125 (mtm)
REVERT: D  165 LEU cc_start: 0.8562 (mt) cc_final: 0.8340 (mt)
REVERT: D  181 GLU cc_start: 0.8199 (mp0) cc_final: 0.7655 (pm20)
REVERT: D  185 LEU cc_start: 0.8676 (tp) cc_final: 0.8434 (tt)
REVERT: D  194 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7549 (ttp80)
  outliers start: 37
  outliers final: 25
  residues processed: 273
  average time/residue: 0.1744
  time to fit residues: 66.0348
Evaluate side-chains
  250 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 220
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 43 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0980
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.092260 restraints weight = 14163.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.095530 restraints weight = 7223.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.097788 restraints weight = 4704.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7754  Z= 0.162
  Angle     :  0.610   7.330  10482  Z= 0.329
  Chirality :  0.045   0.355   1230
  Planarity :  0.004   0.035   1264
  Dihedral  :  9.726 111.567   1040
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 17.22 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.27), residues: 928
  helix:  1.86 (0.21), residues: 562
  sheet:  0.22 (0.72), residues: 58
  loop : -1.05 (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   0.031   0.002   PHE B 143 
 TYR   0.038   0.002   TYR A 206 
 ARG   0.005   0.001   ARG C 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04973 (  483)
  hydrogen bonds       : angle       4.76797 ( 1389)
  covalent geometry    : bond        0.00362 ( 7754)
  covalent geometry    : angle       0.60994 (10482)

*********************** 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
  280 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 232
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A   16 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7634 (mmtt)
REVERT: A  141 TRP cc_start: 0.7789 (m100) cc_final: 0.7411 (m100)
REVERT: A  166 MET cc_start: 0.6306 (mmp) cc_final: 0.5628 (ttm)
REVERT: A  204 PHE cc_start: 0.7558 (m-80) cc_final: 0.6507 (m-80)
REVERT: A  220 ASN cc_start: 0.8108 (m-40) cc_final: 0.7869 (m110)
REVERT: A  221 TRP cc_start: 0.7876 (m100) cc_final: 0.7589 (m100)
REVERT: A  233 PHE cc_start: 0.8254 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  243 LYS cc_start: 0.8072 (mmtt) cc_final: 0.7714 (mmtt)
REVERT: B   11 LEU cc_start: 0.8140 (mt) cc_final: 0.7877 (tt)
REVERT: B   51 TYR cc_start: 0.6979 (m-10) cc_final: 0.6712 (m-80)
REVERT: B   84 GLN cc_start: 0.8391 (tt0) cc_final: 0.7991 (tp40)
REVERT: B  139 ASN cc_start: 0.8237 (t0) cc_final: 0.7571 (t0)
REVERT: B  152 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8747 (mm)
REVERT: B  188 ILE cc_start: 0.6049 (mm) cc_final: 0.5721 (mt)
REVERT: B  200 ASP cc_start: 0.8204 (m-30) cc_final: 0.7865 (t0)
REVERT: B  243 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7918 (mmtt)
REVERT: C    2 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7333 (mtpp)
REVERT: C    4 GLU cc_start: 0.6858 (mp0) cc_final: 0.6439 (mp0)
REVERT: C   43 MET cc_start: 0.8008 (mtm) cc_final: 0.7678 (mtt)
REVERT: C   71 HIS cc_start: 0.6988 (m-70) cc_final: 0.6646 (m90)
REVERT: C   99 TYR cc_start: 0.8028 (t80) cc_final: 0.7621 (t80)
REVERT: C  144 ASP cc_start: 0.8126 (t0) cc_final: 0.7539 (t0)
REVERT: C  181 GLU cc_start: 0.8465 (mp0) cc_final: 0.8128 (pm20)
REVERT: C  186 ILE cc_start: 0.8454 (mm) cc_final: 0.8221 (tt)
REVERT: C  187 CYS cc_start: 0.6418 (t) cc_final: 0.5615 (p)
REVERT: C  204 MET cc_start: 0.6432 (pmm) cc_final: 0.6078 (pmm)
REVERT: D    3 LEU cc_start: 0.8925 (mt) cc_final: 0.8679 (mt)
REVERT: D    4 GLU cc_start: 0.7355 (mp0) cc_final: 0.7014 (mp0)
REVERT: D   64 ASN cc_start: 0.7773 (m-40) cc_final: 0.7413 (m110)
REVERT: D  105 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7640 (m-30)
REVERT: D  124 MET cc_start: 0.8342 (mtm) cc_final: 0.8006 (mtm)
REVERT: D  194 ARG cc_start: 0.7802 (ttp-170) cc_final: 0.7417 (ttp80)
REVERT: D  285 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7131 (t0)
  outliers start: 48
  outliers final: 35
  residues processed: 259
  average time/residue: 0.1581
  time to fit residues: 57.4096
Evaluate side-chains
  257 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 218
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
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  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  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 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  105 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:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
** 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 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 200 GLN
** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3466 r_free = 0.3466 target = 0.110878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.090524 restraints weight = 14181.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.093714 restraints weight = 7242.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.095941 restraints weight = 4721.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.5092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7754  Z= 0.188
  Angle     :  0.637   7.706  10482  Z= 0.338
  Chirality :  0.045   0.332   1230
  Planarity :  0.004   0.035   1264
  Dihedral  :  9.618 106.246   1040
  Min Nonbonded Distance : 1.877

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  7.48 %
    Allowed  : 16.51 %
    Favored  : 76.01 %
  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:  1.04 (0.27), residues: 928
  helix:  1.72 (0.21), residues: 564
  sheet: -0.12 (0.69), residues: 58
  loop : -1.11 (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   0.020   0.002   PHE A 111 
 TYR   0.041   0.002   TYR A 206 
 ARG   0.003   0.001   ARG B  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04871 (  483)
  hydrogen bonds       : angle       4.73032 ( 1389)
  covalent geometry    : bond        0.00429 ( 7754)
  covalent geometry    : angle       0.63736 (10482)

*********************** 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
  283 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 220
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A   16 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7631 (mmtt)
REVERT: A  141 TRP cc_start: 0.7803 (m100) cc_final: 0.7422 (m100)
REVERT: A  166 MET cc_start: 0.6159 (mmp) cc_final: 0.5521 (ttm)
REVERT: A  220 ASN cc_start: 0.8187 (m-40) cc_final: 0.7955 (m110)
REVERT: A  221 TRP cc_start: 0.7907 (m100) cc_final: 0.7667 (m100)
REVERT: A  233 PHE cc_start: 0.8230 (m-80) cc_final: 0.7852 (m-80)
REVERT: B   84 GLN cc_start: 0.8447 (tt0) cc_final: 0.8057 (tp40)
REVERT: B   87 MET cc_start: 0.8279 (mmm) cc_final: 0.7906 (mmm)
REVERT: B  152 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8714 (mm)
REVERT: B  166 MET cc_start: 0.5554 (mmt) cc_final: 0.4738 (ttm)
REVERT: B  200 ASP cc_start: 0.8270 (m-30) cc_final: 0.7736 (t0)
REVERT: B  243 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7953 (mmtt)
REVERT: B  245 ASP cc_start: 0.5338 (m-30) cc_final: 0.5072 (m-30)
REVERT: C    2 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7352 (mtpp)
REVERT: C   43 MET cc_start: 0.8100 (mtm) cc_final: 0.7849 (mtt)
REVERT: C   70 GLU cc_start: 0.7725 (tp30) cc_final: 0.7353 (tp30)
REVERT: C   71 HIS cc_start: 0.6999 (m-70) cc_final: 0.6706 (m90)
REVERT: C   99 TYR cc_start: 0.8203 (t80) cc_final: 0.7925 (t80)
REVERT: C  181 GLU cc_start: 0.8504 (mp0) cc_final: 0.8155 (pm20)
REVERT: C  186 ILE cc_start: 0.8492 (mm) cc_final: 0.8233 (tt)
REVERT: C  187 CYS cc_start: 0.6572 (t) cc_final: 0.5769 (p)
REVERT: C  194 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7423 (ttp80)
REVERT: C  200 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7099 (mt0)
REVERT: C  204 MET cc_start: 0.6584 (pmm) cc_final: 0.6291 (pmm)
REVERT: D    4 GLU cc_start: 0.7355 (mp0) cc_final: 0.6985 (mp0)
REVERT: D  194 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7398 (ttp80)
REVERT: D  285 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.6837 (t0)
  outliers start: 63
  outliers final: 42
  residues processed: 257
  average time/residue: 0.1536
  time to fit residues: 55.9042
Evaluate side-chains
  257 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 211
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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  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  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  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   68 LEU
Chi-restraints excluded: chain C residue  126 GLN
Chi-restraints excluded: chain C residue  132 VAL
Chi-restraints excluded: chain C residue  145 GLU
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   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
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  180 LEU
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:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 56 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 139 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 = 0.3480 r_free = 0.3480 target = 0.111938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.091853 restraints weight = 14038.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.095078 restraints weight = 7054.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.097330 restraints weight = 4565.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.5291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7754  Z= 0.139
  Angle     :  0.596   7.692  10482  Z= 0.317
  Chirality :  0.044   0.306   1230
  Planarity :  0.003   0.034   1264
  Dihedral  :  9.432 102.589   1040
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 18.76 %
    Favored  : 76.01 %
  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:  1.03 (0.27), residues: 928
  helix:  1.72 (0.21), residues: 564
  sheet: -0.10 (0.68), residues: 58
  loop : -1.13 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.002   0.001   HIS D  71 
 PHE   0.019   0.001   PHE A 111 
 TYR   0.044   0.002   TYR A 206 
 ARG   0.002   0.000   ARG A 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04580 (  483)
  hydrogen bonds       : angle       4.62494 ( 1389)
  covalent geometry    : bond        0.00307 ( 7754)
  covalent geometry    : angle       0.59581 (10482)

*********************** 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
  272 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 228
  time to evaluate  : 0.964 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7622 (tt)
REVERT: A   16 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7637 (mmtt)
REVERT: A   31 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8822 (mp)
REVERT: A  141 TRP cc_start: 0.7804 (m100) cc_final: 0.7438 (m100)
REVERT: A  166 MET cc_start: 0.5901 (mmp) cc_final: 0.5176 (ttm)
REVERT: A  220 ASN cc_start: 0.8116 (m-40) cc_final: 0.7915 (m110)
REVERT: A  221 TRP cc_start: 0.7870 (m100) cc_final: 0.7636 (m100)
REVERT: A  233 PHE cc_start: 0.8156 (m-80) cc_final: 0.7786 (m-80)
REVERT: B   60 TRP cc_start: 0.8351 (t60) cc_final: 0.7929 (t60)
REVERT: B   84 GLN cc_start: 0.8416 (tt0) cc_final: 0.8087 (tp40)
REVERT: B  152 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8679 (mm)
REVERT: B  166 MET cc_start: 0.5429 (mmt) cc_final: 0.4634 (ttm)
REVERT: B  188 ILE cc_start: 0.6018 (mm) cc_final: 0.5718 (mt)
REVERT: B  200 ASP cc_start: 0.8207 (m-30) cc_final: 0.7744 (t0)
REVERT: B  243 LYS cc_start: 0.8318 (mmtt) cc_final: 0.7940 (mmtt)
REVERT: B  245 ASP cc_start: 0.5704 (m-30) cc_final: 0.5459 (m-30)
REVERT: C    1 MET cc_start: 0.6869 (tpp) cc_final: 0.6595 (tpt)
REVERT: C    2 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7245 (mtpp)
REVERT: C    3 LEU cc_start: 0.8644 (mt) cc_final: 0.8346 (mt)
REVERT: C    4 GLU cc_start: 0.7181 (mp0) cc_final: 0.6697 (mp0)
REVERT: C   70 GLU cc_start: 0.7737 (tp30) cc_final: 0.7399 (tp30)
REVERT: C   71 HIS cc_start: 0.7039 (m-70) cc_final: 0.6711 (m90)
REVERT: C   99 TYR cc_start: 0.8133 (t80) cc_final: 0.7910 (t80)
REVERT: C  181 GLU cc_start: 0.8509 (mp0) cc_final: 0.8148 (pm20)
REVERT: C  200 GLN cc_start: 0.7631 (mt0) cc_final: 0.7211 (mt0)
REVERT: D    4 GLU cc_start: 0.7322 (mp0) cc_final: 0.6948 (mp0)
REVERT: D  194 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7378 (ttp80)
REVERT: D  285 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.6770 (t0)
  outliers start: 44
  outliers final: 31
  residues processed: 255
  average time/residue: 0.1656
  time to fit residues: 59.3248
Evaluate side-chains
  252 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 216
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
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  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  236 LEU
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   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  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  164 SER
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  197 HIS
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   76 ASP
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:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 47 optimal weight:    0.5980
   chunk 1 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**
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 126 GLN
** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3486 r_free = 0.3486 target = 0.112256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.092211 restraints weight = 14079.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.095437 restraints weight = 7292.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.097653 restraints weight = 4752.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5502

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= 0.142
  Angle     :  0.610   8.254  10482  Z= 0.321
  Chirality :  0.045   0.434   1230
  Planarity :  0.003   0.033   1264
  Dihedral  :  9.325 101.044   1040
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 19.36 %
    Favored  : 74.58 %
  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:  1.04 (0.27), residues: 928
  helix:  1.73 (0.21), residues: 570
  sheet: -0.18 (0.69), residues: 58
  loop : -1.17 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.002   0.001   HIS D  71 
 PHE   0.018   0.001   PHE A 111 
 TYR   0.045   0.002   TYR A 206 
 ARG   0.002   0.000   ARG D 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04473 (  483)
  hydrogen bonds       : angle       4.61453 ( 1389)
  covalent geometry    : bond        0.00319 ( 7754)
  covalent geometry    : angle       0.61046 (10482)

*********************** 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
  276 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 225
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7654 (tt)
REVERT: A   31 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8853 (mp)
REVERT: A  141 TRP cc_start: 0.7845 (m100) cc_final: 0.7458 (m100)
REVERT: A  166 MET cc_start: 0.5888 (mmp) cc_final: 0.5312 (ttm)
REVERT: A  221 TRP cc_start: 0.7819 (m100) cc_final: 0.7581 (m100)
REVERT: A  233 PHE cc_start: 0.8216 (m-80) cc_final: 0.7878 (m-80)
REVERT: B   15 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7182 (m-10)
REVERT: B   60 TRP cc_start: 0.8367 (t60) cc_final: 0.7951 (t60)
REVERT: B   84 GLN cc_start: 0.8370 (tt0) cc_final: 0.8091 (tp40)
REVERT: B  115 HIS cc_start: 0.7680 (t-170) cc_final: 0.7449 (t-170)
REVERT: B  152 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8745 (mm)
REVERT: B  166 MET cc_start: 0.5511 (mmt) cc_final: 0.4811 (ttm)
REVERT: B  188 ILE cc_start: 0.5962 (mm) cc_final: 0.5675 (mt)
REVERT: B  200 ASP cc_start: 0.8163 (m-30) cc_final: 0.7756 (t0)
REVERT: B  243 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7948 (mmtt)
REVERT: B  245 ASP cc_start: 0.5721 (m-30) cc_final: 0.5471 (m-30)
REVERT: C    1 MET cc_start: 0.6579 (tpp) cc_final: 0.6242 (tpt)
REVERT: C    2 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7322 (mtpp)
REVERT: C    3 LEU cc_start: 0.8638 (mt) cc_final: 0.8299 (mt)
REVERT: C    4 GLU cc_start: 0.7220 (mp0) cc_final: 0.6698 (mp0)
REVERT: C   70 GLU cc_start: 0.7640 (tp30) cc_final: 0.7375 (tp30)
REVERT: C   71 HIS cc_start: 0.7076 (m-70) cc_final: 0.6762 (m170)
REVERT: C  126 GLN cc_start: 0.7442 (mt0) cc_final: 0.7190 (mt0)
REVERT: C  181 GLU cc_start: 0.8497 (mp0) cc_final: 0.8220 (pm20)
REVERT: C  202 VAL cc_start: 0.7735 (t) cc_final: 0.7417 (m)
REVERT: D    4 GLU cc_start: 0.7359 (mp0) cc_final: 0.6995 (mp0)
REVERT: D  194 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7422 (ttp80)
REVERT: D  285 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.6600 (t0)
  outliers start: 51
  outliers final: 38
  residues processed: 255
  average time/residue: 0.1658
  time to fit residues: 58.9451
Evaluate side-chains
  260 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 216
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
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   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  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 B residue  241 VAL
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   65 ILE
Chi-restraints excluded: chain D residue   76 ASP
Chi-restraints excluded: chain D residue  132 VAL
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  176 SER
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:    0.0170
   chunk 14 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0470
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.5316

-------------------------------------------------------------------------------
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
D  35 ASN
D  71 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.092167 restraints weight = 14205.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.095319 restraints weight = 7061.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.097694 restraints weight = 4567.984|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.5660

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= 0.128
  Angle     :  0.595   9.406  10482  Z= 0.313
  Chirality :  0.043   0.222   1230
  Planarity :  0.003   0.033   1264
  Dihedral  :  9.172  99.969   1040
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 20.55 %
    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:  1.04 (0.27), residues: 928
  helix:  1.79 (0.21), residues: 564
  sheet: -0.14 (0.69), residues: 58
  loop : -1.24 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.002   0.001   HIS B 115 
 PHE   0.017   0.001   PHE A 111 
 TYR   0.045   0.001   TYR A 206 
 ARG   0.002   0.000   ARG D 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04253 (  483)
  hydrogen bonds       : angle       4.59474 ( 1389)
  covalent geometry    : bond        0.00282 ( 7754)
  covalent geometry    : angle       0.59529 (10482)

*********************** 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
  271 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 229
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A   31 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8794 (mp)
REVERT: A  141 TRP cc_start: 0.7740 (m100) cc_final: 0.7411 (m100)
REVERT: A  166 MET cc_start: 0.5730 (mmp) cc_final: 0.5087 (ttm)
REVERT: A  204 PHE cc_start: 0.7573 (m-80) cc_final: 0.6411 (m-80)
REVERT: A  221 TRP cc_start: 0.7846 (m100) cc_final: 0.7611 (m100)
REVERT: B   12 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6799 (m-80)
REVERT: B   15 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7226 (m-10)
REVERT: B   60 TRP cc_start: 0.8361 (t60) cc_final: 0.8059 (t60)
REVERT: B   84 GLN cc_start: 0.8408 (tt0) cc_final: 0.8072 (tp40)
REVERT: B  115 HIS cc_start: 0.7675 (t-170) cc_final: 0.7456 (t-170)
REVERT: B  152 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8620 (mm)
REVERT: B  166 MET cc_start: 0.5339 (mmt) cc_final: 0.4508 (ttm)
REVERT: B  188 ILE cc_start: 0.5995 (mm) cc_final: 0.5698 (mt)
REVERT: B  243 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7951 (mmtt)
REVERT: B  245 ASP cc_start: 0.5832 (m-30) cc_final: 0.5599 (m-30)
REVERT: C    1 MET cc_start: 0.6528 (tpp) cc_final: 0.6199 (tpt)
REVERT: C    3 LEU cc_start: 0.8561 (mt) cc_final: 0.8196 (mt)
REVERT: C    4 GLU cc_start: 0.7130 (mp0) cc_final: 0.6548 (mp0)
REVERT: C   70 GLU cc_start: 0.7686 (tp30) cc_final: 0.7378 (tp30)
REVERT: C   71 HIS cc_start: 0.7044 (m-70) cc_final: 0.6749 (m170)
REVERT: C  181 GLU cc_start: 0.8532 (mp0) cc_final: 0.8230 (pm20)
REVERT: C  194 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7365 (ttp80)
REVERT: C  202 VAL cc_start: 0.7690 (t) cc_final: 0.7387 (m)
REVERT: C  285 ASN cc_start: 0.7467 (t0) cc_final: 0.6936 (t0)
REVERT: D    4 GLU cc_start: 0.7318 (mp0) cc_final: 0.6916 (mp0)
REVERT: D  194 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7474 (ttp80)
  outliers start: 42
  outliers final: 33
  residues processed: 253
  average time/residue: 0.1654
  time to fit residues: 58.4618
Evaluate side-chains
  257 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 220
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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  101 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  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   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  241 VAL
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   65 ILE
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  176 SER
Chi-restraints excluded: chain D residue  180 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 79 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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
D  35 ASN
D  71 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.111858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.091439 restraints weight = 14299.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.094586 restraints weight = 7163.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.096917 restraints weight = 4659.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.5836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   7754  Z= 0.138
  Angle     :  0.638   9.751  10482  Z= 0.335
  Chirality :  0.044   0.180   1230
  Planarity :  0.003   0.036   1264
  Dihedral  :  9.052  99.676   1040
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 21.73 %
    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:  0.99 (0.27), residues: 928
  helix:  1.68 (0.21), residues: 574
  sheet: -0.10 (0.70), residues: 58
  loop : -1.24 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 223 
 HIS   0.001   0.001   HIS C 178 
 PHE   0.031   0.001   PHE B 218 
 TYR   0.045   0.002   TYR A 206 
 ARG   0.002   0.000   ARG C 189 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  483)
  hydrogen bonds       : angle       4.58646 ( 1389)
  covalent geometry    : bond        0.00319 ( 7754)
  covalent geometry    : angle       0.63806 (10482)

*********************** 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
  267 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 224
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7530 (tt)
REVERT: A   31 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8832 (mp)
REVERT: A  141 TRP cc_start: 0.7755 (m100) cc_final: 0.7424 (m100)
REVERT: A  166 MET cc_start: 0.6059 (mmp) cc_final: 0.5204 (ttm)
REVERT: A  221 TRP cc_start: 0.7852 (m100) cc_final: 0.7637 (m100)
REVERT: B   15 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7277 (m-10)
REVERT: B   60 TRP cc_start: 0.8373 (t60) cc_final: 0.8032 (t60)
REVERT: B   84 GLN cc_start: 0.8399 (tt0) cc_final: 0.8082 (tp40)
REVERT: B  115 HIS cc_start: 0.7711 (t-170) cc_final: 0.7510 (t-170)
REVERT: B  152 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8632 (mm)
REVERT: B  166 MET cc_start: 0.5351 (mmt) cc_final: 0.4438 (ttm)
REVERT: B  188 ILE cc_start: 0.6025 (mm) cc_final: 0.5735 (mt)
REVERT: B  200 ASP cc_start: 0.8273 (m-30) cc_final: 0.7764 (t0)
REVERT: C    3 LEU cc_start: 0.8507 (mt) cc_final: 0.8134 (mt)
REVERT: C    4 GLU cc_start: 0.7117 (mp0) cc_final: 0.6548 (mp0)
REVERT: C   70 GLU cc_start: 0.7650 (tp30) cc_final: 0.7401 (tp30)
REVERT: C   71 HIS cc_start: 0.7100 (m-70) cc_final: 0.6858 (m170)
REVERT: C  181 GLU cc_start: 0.8646 (mp0) cc_final: 0.8341 (pm20)
REVERT: C  186 ILE cc_start: 0.7944 (mm) cc_final: 0.7735 (tp)
REVERT: C  194 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7243 (ttp80)
REVERT: C  202 VAL cc_start: 0.7725 (t) cc_final: 0.7355 (m)
REVERT: C  285 ASN cc_start: 0.7414 (t0) cc_final: 0.6855 (t0)
REVERT: D    4 GLU cc_start: 0.7343 (mp0) cc_final: 0.6955 (mp0)
REVERT: D  194 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7553 (ttp80)
  outliers start: 43
  outliers final: 37
  residues processed: 250
  average time/residue: 0.1643
  time to fit residues: 57.4595
Evaluate side-chains
  254 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 213
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 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  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  223 TRP
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  241 VAL
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  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  176 SER
Chi-restraints excluded: chain D residue  180 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   chunk 54 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 22 optimal weight:    0.0040
   chunk 58 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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
D  35 ASN
** D  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 285 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.112891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.092265 restraints weight = 14212.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.095546 restraints weight = 7131.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.097868 restraints weight = 4605.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.5941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   7754  Z= 0.136
  Angle     :  0.638   9.353  10482  Z= 0.334
  Chirality :  0.045   0.259   1230
  Planarity :  0.003   0.034   1264
  Dihedral  :  8.935  98.337   1040
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.16 %
    Favored  : 72.33 %
  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:  1.00 (0.27), residues: 928
  helix:  1.74 (0.21), residues: 570
  sheet: -0.03 (0.71), residues: 58
  loop : -1.35 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 223 
 HIS   0.001   0.001   HIS A 115 
 PHE   0.032   0.001   PHE B 218 
 TYR   0.046   0.002   TYR A 206 
 ARG   0.001   0.000   ARG A   2 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04145 (  483)
  hydrogen bonds       : angle       4.54060 ( 1389)
  covalent geometry    : bond        0.00308 ( 7754)
  covalent geometry    : angle       0.63806 (10482)

********************** 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
  257 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 219
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A    6 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7472 (tt)
REVERT: A   31 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8835 (mp)
REVERT: A   34 GLN cc_start: 0.7998 (tp-100) cc_final: 0.7757 (mp10)
REVERT: A  141 TRP cc_start: 0.7758 (m100) cc_final: 0.7428 (m100)
REVERT: A  166 MET cc_start: 0.6024 (mmp) cc_final: 0.5182 (ttm)
REVERT: A  204 PHE cc_start: 0.7725 (m-80) cc_final: 0.6611 (m-80)
REVERT: A  221 TRP cc_start: 0.7836 (m100) cc_final: 0.7620 (m100)
REVERT: B   15 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7232 (m-10)
REVERT: B   60 TRP cc_start: 0.8374 (t60) cc_final: 0.8045 (t60)
REVERT: B   84 GLN cc_start: 0.8435 (tt0) cc_final: 0.8133 (tt0)
REVERT: B  152 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8649 (mm)
REVERT: B  166 MET cc_start: 0.5358 (mmt) cc_final: 0.4456 (ttm)
REVERT: C    4 GLU cc_start: 0.7225 (mp0) cc_final: 0.6720 (mp0)
REVERT: C   70 GLU cc_start: 0.7715 (tp30) cc_final: 0.7474 (tp30)
REVERT: C   71 HIS cc_start: 0.7071 (m-70) cc_final: 0.6586 (m170)
REVERT: C  181 GLU cc_start: 0.8459 (mp0) cc_final: 0.8157 (pm20)
REVERT: C  202 VAL cc_start: 0.7733 (t) cc_final: 0.7361 (m)
REVERT: C  285 ASN cc_start: 0.7517 (t0) cc_final: 0.6955 (t0)
REVERT: D  194 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7498 (ttp80)
REVERT: D  285 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.6792 (t0)
  outliers start: 38
  outliers final: 31
  residues processed: 243
  average time/residue: 0.1590
  time to fit residues: 54.3749
Evaluate side-chains
  247 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 211
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 LEU
Chi-restraints excluded: chain A residue   31 ILE
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  101 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  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  190 ARG
Chi-restraints excluded: chain B residue  226 SER
Chi-restraints excluded: chain B residue  229 SER
Chi-restraints excluded: chain B residue  241 VAL
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  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  150 MET
Chi-restraints excluded: chain D residue  155 SER
Chi-restraints excluded: chain D residue  164 SER
Chi-restraints excluded: chain D residue  176 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 88 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 ASN
C 200 GLN
D  35 ASN
** D  49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.113047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.092228 restraints weight = 13985.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.095521 restraints weight = 7175.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.097824 restraints weight = 4660.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7496
moved from start:          0.6030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7754  Z= 0.138
  Angle     :  0.650   9.455  10482  Z= 0.338
  Chirality :  0.046   0.500   1230
  Planarity :  0.003   0.035   1264
  Dihedral  :  8.852  97.989   1040
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 22.80 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.27), residues: 928
  helix:  1.73 (0.21), residues: 574
  sheet: -0.13 (0.72), residues: 58
  loop : -1.29 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 223 
 HIS   0.002   0.001   HIS B 115 
 PHE   0.032   0.001   PHE B 218 
 TYR   0.043   0.002   TYR A 206 
 ARG   0.002   0.000   ARG D 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04113 (  483)
  hydrogen bonds       : angle       4.52135 ( 1389)
  covalent geometry    : bond        0.00314 ( 7754)
  covalent geometry    : angle       0.64971 (10482)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2647.06 seconds
wall clock time: 46 minutes 41.34 seconds (2801.34 seconds total)