Starting phenix.real_space_refine
on Tue Mar  3 19:23:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vxo_21446/03_2026/6vxo_21446.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vxo_21446/03_2026/6vxo_21446.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vxo_21446/03_2026/6vxo_21446.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vxo_21446/03_2026/6vxo_21446.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vxo_21446/03_2026/6vxo_21446.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vxo_21446/03_2026/6vxo_21446.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      24      5.16       5
     C    5548      2.51       5
     N    1184      2.21       5
     O    1280      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8048
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1856
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 7, 'TRANS': 218}
    Chain: "C"
      Number of atoms: 1856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1856
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 7, 'TRANS': 218}
    Chain: "D"
      Number of atoms: 1856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1856
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 7, 'TRANS': 218}
    Chain: "E"
      Number of atoms: 1856
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1856
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 7, 'TRANS': 218}
    Chain: "A"
      Number of atoms: 156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 156
          Unusual residues: {'POV': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 104
          Unusual residues: {'POV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 208
          Unusual residues: {'POV': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "E"
      Number of atoms: 156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 156
          Unusual residues: {'POV': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.83, per 1000 atoms: 0.23
  Number of scatterers: 8048
  At special positions: 0
  Unit cell: (123.654, 123.654, 65.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      12     15.00
     O    1280      8.00
     N    1184      7.00
     C    5548      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 237.0 milliseconds
  

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      74.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 43
      removed outlier: 4.283A  pdb=" N   PHE A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   VAL A  29 " --> pdb=" O   PHE A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 52 through 77
      removed outlier: 3.922A  pdb=" N   PHE A  56 " --> pdb=" O   HIS A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 106
      removed outlier: 3.545A  pdb=" N   TRP A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 122
      removed outlier: 3.893A  pdb=" N   LEU A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ARG A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 117 through 122'
    Processing helix  chain 'A' and resid 125 through 130
    Processing helix  chain 'A' and resid 130 through 143
    Processing helix  chain 'A' and resid 148 through 169
      removed outlier: 3.665A  pdb=" N   MET A 167 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 168 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 187 through 192
      removed outlier: 3.744A  pdb=" N   VAL A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 211 through 235
      removed outlier: 3.959A  pdb=" N   PHE A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 23 through 43
      removed outlier: 4.284A  pdb=" N   PHE C  27 " --> pdb=" O   ARG C  23 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   VAL C  29 " --> pdb=" O   PHE C  25 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 52
    Processing helix  chain 'C' and resid 52 through 77
      removed outlier: 3.923A  pdb=" N   PHE C  56 " --> pdb=" O   HIS C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 106
      removed outlier: 3.545A  pdb=" N   TRP C  91 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 122
      removed outlier: 3.893A  pdb=" N   LEU C 121 " --> pdb=" O   ILE C 117 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ARG C 122 " --> pdb=" O   LEU C 118 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 117 through 122'
    Processing helix  chain 'C' and resid 125 through 130
    Processing helix  chain 'C' and resid 130 through 143
    Processing helix  chain 'C' and resid 148 through 169
      removed outlier: 3.664A  pdb=" N   MET C 167 " --> pdb=" O   VAL C 163 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU C 168 " --> pdb=" O   ILE C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 187
    Processing helix  chain 'C' and resid 187 through 192
      removed outlier: 3.745A  pdb=" N   VAL C 191 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 201 through 206
    Processing helix  chain 'C' and resid 208 through 210
      No H-bonds generated for 'chain 'C' and resid 208 through 210'
    Processing helix  chain 'C' and resid 211 through 235
      removed outlier: 3.960A  pdb=" N   PHE C 215 " --> pdb=" O   SER C 211 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU C 220 " --> pdb=" O   VAL C 216 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 43
      removed outlier: 4.284A  pdb=" N   PHE D  27 " --> pdb=" O   ARG D  23 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   VAL D  29 " --> pdb=" O   PHE D  25 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 52
    Processing helix  chain 'D' and resid 52 through 77
      removed outlier: 3.922A  pdb=" N   PHE D  56 " --> pdb=" O   HIS D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 106
      removed outlier: 3.545A  pdb=" N   TRP D  91 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 122
      removed outlier: 3.893A  pdb=" N   LEU D 121 " --> pdb=" O   ILE D 117 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ARG D 122 " --> pdb=" O   LEU D 118 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 117 through 122'
    Processing helix  chain 'D' and resid 125 through 130
    Processing helix  chain 'D' and resid 130 through 143
    Processing helix  chain 'D' and resid 148 through 169
      removed outlier: 3.664A  pdb=" N   MET D 167 " --> pdb=" O   VAL D 163 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU D 168 " --> pdb=" O   ILE D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 187
    Processing helix  chain 'D' and resid 187 through 192
      removed outlier: 3.745A  pdb=" N   VAL D 191 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 201 through 206
    Processing helix  chain 'D' and resid 208 through 210
      No H-bonds generated for 'chain 'D' and resid 208 through 210'
    Processing helix  chain 'D' and resid 211 through 235
      removed outlier: 3.959A  pdb=" N   PHE D 215 " --> pdb=" O   SER D 211 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU D 220 " --> pdb=" O   VAL D 216 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 23 through 43
      removed outlier: 4.285A  pdb=" N   PHE E  27 " --> pdb=" O   ARG E  23 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   VAL E  29 " --> pdb=" O   PHE E  25 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 52
    Processing helix  chain 'E' and resid 52 through 77
      removed outlier: 3.923A  pdb=" N   PHE E  56 " --> pdb=" O   HIS E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 106
      removed outlier: 3.546A  pdb=" N   TRP E  91 " --> pdb=" O   SER E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 117 through 122
      removed outlier: 3.892A  pdb=" N   LEU E 121 " --> pdb=" O   ILE E 117 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   ARG E 122 " --> pdb=" O   LEU E 118 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 117 through 122'
    Processing helix  chain 'E' and resid 125 through 130
    Processing helix  chain 'E' and resid 130 through 143
    Processing helix  chain 'E' and resid 148 through 169
      removed outlier: 3.665A  pdb=" N   MET E 167 " --> pdb=" O   VAL E 163 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU E 168 " --> pdb=" O   ILE E 164 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 182 through 187
    Processing helix  chain 'E' and resid 187 through 192
      removed outlier: 3.744A  pdb=" N   VAL E 191 " --> pdb=" O   LEU E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 201 through 206
    Processing helix  chain 'E' and resid 208 through 210
      No H-bonds generated for 'chain 'E' and resid 208 through 210'
    Processing helix  chain 'E' and resid 211 through 235
      removed outlier: 3.959A  pdb=" N   PHE E 215 " --> pdb=" O   SER E 211 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU E 220 " --> pdb=" O   VAL E 216 " (cutoff:3.500A)

    428 hydrogen bonds defined for protein.
    1284 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1084
        1.30 -     1.43: 2299
        1.43 -     1.55: 4723
        1.55 -     1.68: 90
        1.68 -     1.80: 48
  Bond restraints: 8244
  Sorted by residual:
  bond pdb=" C31 POV D 302 "
       pdb=" O31 POV D 302 "
    ideal  model  delta    sigma   weight residual
    1.327  1.424 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" C31 POV C 302 "
       pdb=" O31 POV C 302 "
    ideal  model  delta    sigma   weight residual
    1.327  1.424 -0.097 2.00e-02 2.50e+03 2.34e+01
  bond pdb=" C31 POV E 302 "
       pdb=" O31 POV E 302 "
    ideal  model  delta    sigma   weight residual
    1.327  1.423 -0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" C31 POV A 303 "
       pdb=" O31 POV A 303 "
    ideal  model  delta    sigma   weight residual
    1.327  1.423 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C31 POV C 301 "
       pdb=" O31 POV C 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.423 -0.096 2.00e-02 2.50e+03 2.28e+01
  ... (remaining 8239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 10386
        2.32 -     4.65: 483
        4.65 -     6.97: 163
        6.97 -     9.30: 48
        9.30 -    11.62: 32
  Bond angle restraints: 11112
  Sorted by residual:
  angle pdb=" N   VAL A 114 "
        pdb=" CA  VAL A 114 "
        pdb=" C   VAL A 114 "
      ideal   model   delta    sigma   weight residual
     111.91  107.01    4.90 8.90e-01 1.26e+00 3.03e+01
  angle pdb=" N   VAL C 114 "
        pdb=" CA  VAL C 114 "
        pdb=" C   VAL C 114 "
      ideal   model   delta    sigma   weight residual
     111.91  107.03    4.88 8.90e-01 1.26e+00 3.01e+01
  angle pdb=" N   VAL E 114 "
        pdb=" CA  VAL E 114 "
        pdb=" C   VAL E 114 "
      ideal   model   delta    sigma   weight residual
     111.91  107.03    4.88 8.90e-01 1.26e+00 3.01e+01
  angle pdb=" N   VAL D 114 "
        pdb=" CA  VAL D 114 "
        pdb=" C   VAL D 114 "
      ideal   model   delta    sigma   weight residual
     111.91  107.04    4.87 8.90e-01 1.26e+00 3.00e+01
  angle pdb=" O13 POV A 303 "
        pdb=" P   POV A 303 "
        pdb=" O14 POV A 303 "
      ideal   model   delta    sigma   weight residual
     121.11  109.49   11.62 3.00e+00 1.11e-01 1.50e+01
  ... (remaining 11107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.08: 4071
       24.08 -    48.16: 594
       48.16 -    72.24: 175
       72.24 -    96.32: 48
       96.32 -   120.40: 12
  Dihedral angle restraints: 4900
    sinusoidal: 2232
      harmonic: 2668
  Sorted by residual:
  dihedral pdb=" CA  VAL C 109 "
           pdb=" C   VAL C 109 "
           pdb=" N   GLU C 110 "
           pdb=" CA  GLU C 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.80   23.20     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  VAL E 235 "
           pdb=" C   VAL E 235 "
           pdb=" N   ASN E 236 "
           pdb=" CA  ASN E 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.80   23.20     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  VAL D 235 "
           pdb=" C   VAL D 235 "
           pdb=" N   ASN D 236 "
           pdb=" CA  ASN D 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.80   23.20     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 4897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 587
       0.027 -    0.053: 338
       0.053 -    0.079: 207
       0.079 -    0.106: 93
       0.106 -    0.132: 35
  Chirality restraints: 1260
  Sorted by residual:
  chirality pdb=" CA  VAL A 235 "
            pdb=" N   VAL A 235 "
            pdb=" C   VAL A 235 "
            pdb=" CB  VAL A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  VAL D 235 "
            pdb=" N   VAL D 235 "
            pdb=" C   VAL D 235 "
            pdb=" CB  VAL D 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.27e-01
  chirality pdb=" CA  VAL C 235 "
            pdb=" N   VAL C 235 "
            pdb=" C   VAL C 235 "
            pdb=" CB  VAL C 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 1257 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE D 234 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   ILE D 234 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE D 234 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL D 235 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 234 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   ILE C 234 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ILE C 234 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL C 235 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 234 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.80e+00
        pdb=" C   ILE A 234 "    0.029 2.00e-02 2.50e+03
        pdb=" O   ILE A 234 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL A 235 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 307
        2.68 -     3.24: 8646
        3.24 -     3.79: 12731
        3.79 -     4.35: 15410
        4.35 -     4.90: 25309
  Nonbonded interactions: 62403
  Sorted by model distance:
  nonbonded pdb=" O   TYR D 214 "
            pdb=" OG  SER D 217 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" O   TYR A 214 "
            pdb=" OG  SER A 217 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" O   TYR E 214 "
            pdb=" OG  SER E 217 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" O   TYR C 214 "
            pdb=" OG  SER C 217 "
     model   vdw
     2.126 3.040
  nonbonded pdb=" O   PHE E 161 "
            pdb=" OH  TYR E 214 "
     model   vdw
     2.219 3.040
  ... (remaining 62398 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 15 through 302)
  selection = chain 'C'
  selection = (chain 'D' and resid 15 through 302)
  selection = (chain 'E' and resid 15 through 302)
}

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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.890
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
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      :  0.012   0.097   8244  Z= 0.586
  Angle     :  1.401  11.619  11112  Z= 0.585
  Chirality :  0.047   0.132   1260
  Planarity :  0.005   0.035   1272
  Dihedral  : 24.970 120.396   3156
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 12.17 %
    Favored  : 87.39 %
  Rotamer:
    Outliers : 21.57 %
    Allowed  : 21.08 %
    Favored  : 57.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.90 (0.24), residues: 896
  helix: -1.88 (0.17), residues: 640
  sheet:  None (None), residues: 0
  loop : -4.16 (0.33), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 122 
 TYR   0.007   0.001   TYR A 159 
 PHE   0.017   0.002   PHE C 205 
 TRP   0.011   0.001   TRP E  65 
 HIS   0.003   0.001   HIS C 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.01229 ( 8244)
  covalent geometry    : angle       1.40070 (11112)
  hydrogen bonds       : bond        0.17884 (  428)
  hydrogen bonds       : angle       7.61056 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 176
    poor density    : 207
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 TYR cc_start: 0.8605 (m-80) cc_final: 0.8347 (m-80)
REVERT: A   47 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7838 (ttm-80)
REVERT: A   54 TRP cc_start: 0.7193 (p-90) cc_final: 0.6970 (p-90)
REVERT: A   63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9139 (mm)
REVERT: A   65 TRP cc_start: 0.8015 (m100) cc_final: 0.7668 (t-100)
REVERT: A   70 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8263 (tp30)
REVERT: A  103 GLU cc_start: 0.8881 (tp30) cc_final: 0.8587 (tp30)
REVERT: A  230 PHE cc_start: 0.7810 (t80) cc_final: 0.7605 (t80)
REVERT: C   45 TYR cc_start: 0.8575 (m-80) cc_final: 0.8319 (m-80)
REVERT: C   47 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7791 (ttm-80)
REVERT: C   54 TRP cc_start: 0.7194 (p-90) cc_final: 0.6965 (p-90)
REVERT: C   63 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9140 (mm)
REVERT: C   65 TRP cc_start: 0.8002 (m100) cc_final: 0.7624 (t-100)
REVERT: C   70 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8243 (tp30)
REVERT: C  103 GLU cc_start: 0.8868 (tp30) cc_final: 0.8620 (tp30)
REVERT: C  115 LEU cc_start: 0.8801 (mt) cc_final: 0.8526 (mt)
REVERT: C  230 PHE cc_start: 0.7810 (t80) cc_final: 0.7598 (t80)
REVERT: D   45 TYR cc_start: 0.8603 (m-80) cc_final: 0.8339 (m-80)
REVERT: D   47 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7809 (ttm-80)
REVERT: D   54 TRP cc_start: 0.7218 (p-90) cc_final: 0.6990 (p-90)
REVERT: D   63 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9132 (mm)
REVERT: D   65 TRP cc_start: 0.7986 (m100) cc_final: 0.7618 (t-100)
REVERT: D   70 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8265 (tp30)
REVERT: D  103 GLU cc_start: 0.8885 (tp30) cc_final: 0.8677 (tp30)
REVERT: D  115 LEU cc_start: 0.8844 (mt) cc_final: 0.8593 (mt)
REVERT: D  230 PHE cc_start: 0.7821 (t80) cc_final: 0.7598 (t80)
REVERT: E   45 TYR cc_start: 0.8632 (m-80) cc_final: 0.8402 (m-80)
REVERT: E   47 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7820 (ttm-80)
REVERT: E   54 TRP cc_start: 0.7227 (p-90) cc_final: 0.7024 (p-90)
REVERT: E   63 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9115 (mm)
REVERT: E   65 TRP cc_start: 0.8109 (m100) cc_final: 0.7658 (t-100)
REVERT: E   70 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8274 (tp30)
REVERT: E  115 LEU cc_start: 0.8688 (mt) cc_final: 0.8449 (mt)
REVERT: E  230 PHE cc_start: 0.7851 (t80) cc_final: 0.7623 (t80)
  outliers start: 176
  outliers final: 141
  residues processed: 336
  average time/residue: 0.0623
  time to fit residues: 31.1648
Evaluate side-chains
  329 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 149
    poor density    : 180
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   47 ARG
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   90 ASN
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  110 GLU
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  157 PHE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  223 THR
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   30 ILE
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   47 ARG
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   68 THR
Chi-restraints excluded: chain C residue   82 SER
Chi-restraints excluded: chain C residue   90 ASN
Chi-restraints excluded: chain C residue   96 ILE
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  110 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  130 VAL
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  144 ILE
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  157 PHE
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  181 GLN
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  189 GLN
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  223 THR
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain C residue  235 VAL
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   20 VAL
Chi-restraints excluded: chain D residue   26 THR
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   30 ILE
Chi-restraints excluded: chain D residue   43 GLU
Chi-restraints excluded: chain D residue   47 ARG
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   68 THR
Chi-restraints excluded: chain D residue   82 SER
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  121 LEU
Chi-restraints excluded: chain D residue  123 VAL
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  130 VAL
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain D residue  157 PHE
Chi-restraints excluded: chain D residue  180 LEU
Chi-restraints excluded: chain D residue  181 GLN
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  184 LEU
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  189 GLN
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain D residue  223 THR
Chi-restraints excluded: chain D residue  228 ASN
Chi-restraints excluded: chain D residue  235 VAL
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   20 VAL
Chi-restraints excluded: chain E residue   26 THR
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   30 ILE
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   47 ARG
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   68 THR
Chi-restraints excluded: chain E residue   82 SER
Chi-restraints excluded: chain E residue   90 ASN
Chi-restraints excluded: chain E residue   96 ILE
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  110 GLU
Chi-restraints excluded: chain E residue  121 LEU
Chi-restraints excluded: chain E residue  123 VAL
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  130 VAL
Chi-restraints excluded: chain E residue  141 VAL
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  144 ILE
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  157 PHE
Chi-restraints excluded: chain E residue  181 GLN
Chi-restraints excluded: chain E residue  182 LEU
Chi-restraints excluded: chain E residue  184 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  189 GLN
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Chi-restraints excluded: chain E residue  223 THR
Chi-restraints excluded: chain E residue  228 ASN
Chi-restraints excluded: chain E residue  238 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A  90 ASN
A 170 GLN
A 181 GLN
A 237 ASN
C  90 ASN
C 170 GLN
C 181 GLN
C 237 ASN
D  90 ASN
D 170 GLN
D 181 GLN
D 237 ASN
E  90 ASN
E 170 GLN
E 181 GLN
E 237 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.120276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.095578 restraints weight = 16094.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.098732 restraints weight = 7162.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.100801 restraints weight = 4402.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.101993 restraints weight = 3300.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.102740 restraints weight = 2807.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8244  Z= 0.144
  Angle     :  0.622   5.904  11112  Z= 0.321
  Chirality :  0.041   0.154   1260
  Planarity :  0.003   0.019   1272
  Dihedral  : 23.639 109.875   1756
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  9.80 %
    Allowed  : 23.53 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.28), residues: 896
  helix:  0.26 (0.21), residues: 616
  sheet:  None (None), residues: 0
  loop : -2.89 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  74 
 TYR   0.011   0.001   TYR D 214 
 PHE   0.014   0.001   PHE A 205 
 TRP   0.011   0.001   TRP E  65 
 HIS   0.002   0.001   HIS C  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8244)
  covalent geometry    : angle       0.62219 (11112)
  hydrogen bonds       : bond        0.04363 (  428)
  hydrogen bonds       : angle       4.29322 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 221
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 TYR cc_start: 0.8323 (m-80) cc_final: 0.7978 (m-80)
REVERT: A   53 LYS cc_start: 0.8450 (ttpt) cc_final: 0.8171 (tptp)
REVERT: A   65 TRP cc_start: 0.8063 (m100) cc_final: 0.7707 (t-100)
REVERT: A  207 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7623 (mm-30)
REVERT: C   45 TYR cc_start: 0.8332 (m-80) cc_final: 0.7986 (m-80)
REVERT: C   53 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8209 (tptp)
REVERT: C   54 TRP cc_start: 0.7002 (p-90) cc_final: 0.6800 (p-90)
REVERT: C   65 TRP cc_start: 0.8053 (m100) cc_final: 0.7702 (t-100)
REVERT: C  207 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7586 (mm-30)
REVERT: D   45 TYR cc_start: 0.8361 (m-80) cc_final: 0.8016 (m-80)
REVERT: D   53 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8147 (tptp)
REVERT: D   65 TRP cc_start: 0.8051 (m100) cc_final: 0.7689 (t-100)
REVERT: D  207 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7552 (mm-30)
REVERT: E   45 TYR cc_start: 0.8350 (m-80) cc_final: 0.8031 (m-80)
REVERT: E   65 TRP cc_start: 0.8093 (m100) cc_final: 0.7729 (t-100)
REVERT: E  207 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7587 (mm-30)
  outliers start: 80
  outliers final: 40
  residues processed: 288
  average time/residue: 0.0568
  time to fit residues: 25.0071
Evaluate side-chains
  252 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 212
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  189 GLN
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  189 GLN
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Chi-restraints excluded: chain E residue  238 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:   20.0000
   chunk 87 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 47 optimal weight:    0.1980
   chunk 83 optimal weight:    0.0770
   chunk 67 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 82 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.4738

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

Flipped N/Q/H residues before XYZ refinement:
A 228 ASN
C 228 ASN
D 228 ASN
E 228 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.124410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.099836 restraints weight = 15642.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.103056 restraints weight = 6952.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.105148 restraints weight = 4255.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.106445 restraints weight = 3180.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.106998 restraints weight = 2690.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8244  Z= 0.112
  Angle     :  0.612   7.577  11112  Z= 0.307
  Chirality :  0.043   0.172   1260
  Planarity :  0.003   0.019   1272
  Dihedral  : 21.607 107.074   1549
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers : 10.05 %
    Allowed  : 26.59 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.30), residues: 896
  helix:  0.63 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.05 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 202 
 TYR   0.004   0.001   TYR C 214 
 PHE   0.026   0.001   PHE C  94 
 TRP   0.009   0.001   TRP E  65 
 HIS   0.001   0.000   HIS C  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8244)
  covalent geometry    : angle       0.61180 (11112)
  hydrogen bonds       : bond        0.03836 (  428)
  hydrogen bonds       : angle       3.83515 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 244
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 TYR cc_start: 0.8153 (m-80) cc_final: 0.7749 (m-80)
REVERT: A   65 TRP cc_start: 0.7934 (m100) cc_final: 0.7619 (t-100)
REVERT: A  158 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.9077 (m-80)
REVERT: A  202 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8776 (tpp-160)
REVERT: C   45 TYR cc_start: 0.8184 (m-80) cc_final: 0.7758 (m-80)
REVERT: C   55 LEU cc_start: 0.9017 (tp) cc_final: 0.8816 (pt)
REVERT: C   63 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9141 (mm)
REVERT: C   65 TRP cc_start: 0.7968 (m100) cc_final: 0.7581 (t-100)
REVERT: C   73 MET cc_start: 0.6407 (tpt) cc_final: 0.6143 (tpt)
REVERT: C  138 ASP cc_start: 0.8234 (t0) cc_final: 0.8027 (t0)
REVERT: C  158 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9132 (m-80)
REVERT: C  202 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8812 (tpp-160)
REVERT: D   63 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9183 (mm)
REVERT: D   65 TRP cc_start: 0.7983 (m100) cc_final: 0.7601 (t-100)
REVERT: D  138 ASP cc_start: 0.8218 (t0) cc_final: 0.8006 (t0)
REVERT: D  158 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.9131 (m-80)
REVERT: D  207 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: E   45 TYR cc_start: 0.8143 (m-80) cc_final: 0.7734 (m-80)
REVERT: E   65 TRP cc_start: 0.8060 (m100) cc_final: 0.7633 (t-100)
REVERT: E  138 ASP cc_start: 0.8207 (t0) cc_final: 0.8000 (t0)
REVERT: E  158 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9080 (m-80)
REVERT: E  202 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8772 (tpp-160)
  outliers start: 82
  outliers final: 44
  residues processed: 311
  average time/residue: 0.0616
  time to fit residues: 28.4428
Evaluate side-chains
  253 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 200
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  158 PHE
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  238 VAL
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  202 ARG
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  238 VAL
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  158 PHE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  202 ARG
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Chi-restraints excluded: chain E residue  238 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 72 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** D  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.120585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.095948 restraints weight = 16051.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.099057 restraints weight = 7243.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.101121 restraints weight = 4503.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.102377 restraints weight = 3409.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.102881 restraints weight = 2900.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8244  Z= 0.156
  Angle     :  0.692  13.090  11112  Z= 0.336
  Chirality :  0.044   0.163   1260
  Planarity :  0.003   0.022   1272
  Dihedral  : 21.070 106.822   1536
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers : 10.78 %
    Allowed  : 25.86 %
    Favored  : 63.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.04 (0.29), residues: 896
  helix:  0.89 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.19 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 116 
 TYR   0.014   0.002   TYR A 214 
 PHE   0.030   0.002   PHE E  94 
 TRP   0.012   0.001   TRP C  65 
 HIS   0.002   0.001   HIS D  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8244)
  covalent geometry    : angle       0.69179 (11112)
  hydrogen bonds       : bond        0.04141 (  428)
  hydrogen bonds       : angle       3.90352 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 204
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 TYR cc_start: 0.8210 (m-80) cc_final: 0.7772 (m-80)
REVERT: A   63 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9095 (mm)
REVERT: A   73 MET cc_start: 0.6557 (tpt) cc_final: 0.6345 (tpt)
REVERT: A  158 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.9099 (m-80)
REVERT: C   45 TYR cc_start: 0.8191 (m-80) cc_final: 0.7743 (m-80)
REVERT: C   63 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9241 (mm)
REVERT: C   65 TRP cc_start: 0.8023 (m100) cc_final: 0.7816 (t-100)
REVERT: C   73 MET cc_start: 0.6385 (tpt) cc_final: 0.6140 (tpt)
REVERT: C  138 ASP cc_start: 0.8270 (t0) cc_final: 0.8055 (t0)
REVERT: C  158 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.9138 (m-80)
REVERT: D   65 TRP cc_start: 0.8009 (m100) cc_final: 0.7613 (t-100)
REVERT: D  158 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9132 (m-80)
REVERT: D  207 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7555 (mm-30)
REVERT: E   45 TYR cc_start: 0.8276 (m-80) cc_final: 0.7842 (m-80)
REVERT: E   60 ASP cc_start: 0.8675 (t70) cc_final: 0.8382 (t0)
REVERT: E   63 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9103 (mm)
REVERT: E  158 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9120 (m-80)
  outliers start: 88
  outliers final: 64
  residues processed: 273
  average time/residue: 0.0562
  time to fit residues: 23.7001
Evaluate side-chains
  275 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 204
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   91 TRP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  109 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  158 PHE
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   91 TRP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  109 VAL
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   55 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   91 TRP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  158 PHE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain D residue  228 ASN
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   55 LEU
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   91 TRP
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  109 VAL
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Chi-restraints excluded: chain E residue  228 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   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  36 ASN
** C  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  36 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.122140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.096853 restraints weight = 15575.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.100090 restraints weight = 6889.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.102239 restraints weight = 4258.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.103526 restraints weight = 3220.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.104279 restraints weight = 2744.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8244  Z= 0.126
  Angle     :  0.677  12.619  11112  Z= 0.325
  Chirality :  0.043   0.167   1260
  Planarity :  0.003   0.026   1272
  Dihedral  : 20.159 106.561   1532
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers : 10.17 %
    Allowed  : 28.06 %
    Favored  : 61.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.29), residues: 896
  helix:  0.91 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -2.05 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 202 
 TYR   0.009   0.001   TYR A 214 
 PHE   0.026   0.001   PHE E  94 
 TRP   0.010   0.001   TRP D  65 
 HIS   0.001   0.001   HIS E  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8244)
  covalent geometry    : angle       0.67749 (11112)
  hydrogen bonds       : bond        0.03929 (  428)
  hydrogen bonds       : angle       3.69032 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 219
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 TYR cc_start: 0.8173 (m-80) cc_final: 0.7722 (m-80)
REVERT: A   54 TRP cc_start: 0.7019 (p-90) cc_final: 0.6781 (p-90)
REVERT: A   63 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9115 (mm)
REVERT: A  158 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9105 (m-80)
REVERT: A  201 MET cc_start: 0.8516 (ttp) cc_final: 0.8311 (ttp)
REVERT: C   45 TYR cc_start: 0.8165 (m-80) cc_final: 0.7704 (m-80)
REVERT: C  158 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.9130 (m-80)
REVERT: D   45 TYR cc_start: 0.8221 (m-80) cc_final: 0.7836 (m-80)
REVERT: D   54 TRP cc_start: 0.6988 (p-90) cc_final: 0.6749 (p-90)
REVERT: D  106 LEU cc_start: 0.8935 (tp) cc_final: 0.8731 (tt)
REVERT: D  158 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9159 (m-80)
REVERT: E   45 TYR cc_start: 0.8202 (m-80) cc_final: 0.7751 (m-80)
REVERT: E   63 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9088 (mm)
REVERT: E  154 MET cc_start: 0.8372 (tpt) cc_final: 0.8132 (tpt)
REVERT: E  158 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.9064 (m-80)
REVERT: E  201 MET cc_start: 0.8533 (ttp) cc_final: 0.8322 (ttp)
  outliers start: 83
  outliers final: 66
  residues processed: 282
  average time/residue: 0.0535
  time to fit residues: 23.1141
Evaluate side-chains
  278 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 206
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain A residue   91 TRP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  158 PHE
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 PHE
Chi-restraints excluded: chain C residue   91 TRP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   91 TRP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain D residue  158 PHE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain D residue  228 ASN
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   91 TRP
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Chi-restraints excluded: chain E residue  228 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 83 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   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  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.122830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.097574 restraints weight = 15513.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.100816 restraints weight = 6898.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.102971 restraints weight = 4259.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.104204 restraints weight = 3219.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.104873 restraints weight = 2759.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8244  Z= 0.130
  Angle     :  0.718  13.061  11112  Z= 0.340
  Chirality :  0.043   0.171   1260
  Planarity :  0.003   0.029   1272
  Dihedral  : 19.071 105.740   1525
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers : 10.29 %
    Allowed  : 28.80 %
    Favored  : 60.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.29), residues: 896
  helix:  0.85 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -1.78 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 202 
 TYR   0.012   0.001   TYR E 214 
 PHE   0.024   0.001   PHE E  94 
 TRP   0.012   0.001   TRP C  54 
 HIS   0.001   0.001   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8244)
  covalent geometry    : angle       0.71821 (11112)
  hydrogen bonds       : bond        0.03937 (  428)
  hydrogen bonds       : angle       3.65738 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 219
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7521 (pp20)
REVERT: A   45 TYR cc_start: 0.8125 (m-80) cc_final: 0.7649 (m-80)
REVERT: A   63 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9045 (mm)
REVERT: A  158 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9079 (m-80)
REVERT: A  201 MET cc_start: 0.8567 (ttp) cc_final: 0.8359 (ttp)
REVERT: A  220 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8690 (mm)
REVERT: C   43 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7470 (pp20)
REVERT: C   45 TYR cc_start: 0.8101 (m-80) cc_final: 0.7595 (m-80)
REVERT: C   63 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9139 (mm)
REVERT: C   73 MET cc_start: 0.6415 (tpt) cc_final: 0.6210 (tpt)
REVERT: C  158 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.9087 (m-80)
REVERT: C  220 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: C  230 PHE cc_start: 0.7697 (t80) cc_final: 0.7297 (t80)
REVERT: D   45 TYR cc_start: 0.8213 (m-80) cc_final: 0.7832 (m-80)
REVERT: D   54 TRP cc_start: 0.6977 (p-90) cc_final: 0.6745 (p-90)
REVERT: D   63 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9150 (mm)
REVERT: D  158 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.9122 (m-80)
REVERT: D  220 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8725 (mm)
REVERT: D  230 PHE cc_start: 0.7656 (t80) cc_final: 0.7165 (t80)
REVERT: E   45 TYR cc_start: 0.8150 (m-80) cc_final: 0.7658 (m-80)
REVERT: E   63 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8980 (mm)
REVERT: E  154 MET cc_start: 0.8311 (tpt) cc_final: 0.8058 (tpt)
REVERT: E  158 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.9072 (m-80)
REVERT: E  220 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8666 (mm)
  outliers start: 84
  outliers final: 63
  residues processed: 279
  average time/residue: 0.0626
  time to fit residues: 26.3783
Evaluate side-chains
  281 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 204
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   91 TRP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  158 PHE
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 PHE
Chi-restraints excluded: chain C residue   91 TRP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 PHE
Chi-restraints excluded: chain D residue   91 TRP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  109 VAL
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain D residue  158 PHE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   26 THR
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 PHE
Chi-restraints excluded: chain E residue   91 TRP
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 72 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   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  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.123480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.098504 restraints weight = 15687.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.101732 restraints weight = 6982.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.103897 restraints weight = 4305.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.105123 restraints weight = 3231.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.105950 restraints weight = 2754.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8244  Z= 0.133
  Angle     :  0.729  14.261  11112  Z= 0.345
  Chirality :  0.043   0.173   1260
  Planarity :  0.003   0.040   1272
  Dihedral  : 18.472 106.693   1525
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers : 10.29 %
    Allowed  : 31.00 %
    Favored  : 58.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.29), residues: 896
  helix:  0.90 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -1.59 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 202 
 TYR   0.011   0.001   TYR D 214 
 PHE   0.021   0.001   PHE E  94 
 TRP   0.005   0.001   TRP C  54 
 HIS   0.001   0.001   HIS C  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8244)
  covalent geometry    : angle       0.72873 (11112)
  hydrogen bonds       : bond        0.03911 (  428)
  hydrogen bonds       : angle       3.73952 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 212
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 VAL cc_start: 0.9242 (OUTLIER) cc_final: 0.8822 (p)
REVERT: A   43 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7631 (pp20)
REVERT: A   63 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8945 (mm)
REVERT: A  158 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.9058 (m-80)
REVERT: A  201 MET cc_start: 0.8556 (ttp) cc_final: 0.8344 (ttp)
REVERT: A  220 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8574 (mt)
REVERT: C   43 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7669 (pp20)
REVERT: C   63 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9067 (mm)
REVERT: C  158 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.9085 (m-80)
REVERT: D   45 TYR cc_start: 0.8132 (m-80) cc_final: 0.7753 (m-80)
REVERT: D   63 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9058 (mm)
REVERT: D  158 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.9064 (m-80)
REVERT: D  230 PHE cc_start: 0.7613 (t80) cc_final: 0.7158 (t80)
REVERT: E   40 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8763 (p)
REVERT: E   43 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7616 (pp20)
REVERT: E   45 TYR cc_start: 0.8045 (m-80) cc_final: 0.7509 (m-80)
REVERT: E   63 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8950 (mm)
REVERT: E  154 MET cc_start: 0.8317 (tpt) cc_final: 0.8054 (tpt)
REVERT: E  158 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9041 (m-80)
  outliers start: 84
  outliers final: 63
  residues processed: 271
  average time/residue: 0.0620
  time to fit residues: 25.2174
Evaluate side-chains
  280 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 203
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain A residue   91 TRP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  158 PHE
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 PHE
Chi-restraints excluded: chain C residue   91 TRP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 PHE
Chi-restraints excluded: chain D residue   91 TRP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain D residue  158 PHE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   26 THR
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 PHE
Chi-restraints excluded: chain E residue   91 TRP
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 67 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.120224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.095269 restraints weight = 15724.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.098485 restraints weight = 7120.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.100574 restraints weight = 4433.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.101775 restraints weight = 3351.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.102550 restraints weight = 2873.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8244  Z= 0.170
  Angle     :  0.746  12.734  11112  Z= 0.360
  Chirality :  0.045   0.184   1260
  Planarity :  0.003   0.034   1272
  Dihedral  : 18.507 111.906   1524
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.15 %
    Favored  : 90.85 %
  Rotamer:
    Outliers : 10.54 %
    Allowed  : 31.37 %
    Favored  : 58.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.29), residues: 896
  helix:  0.81 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.61 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.012   0.002   TYR D 214 
 PHE   0.020   0.001   PHE E  94 
 TRP   0.005   0.001   TRP C 212 
 HIS   0.002   0.001   HIS E  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 8244)
  covalent geometry    : angle       0.74613 (11112)
  hydrogen bonds       : bond        0.04061 (  428)
  hydrogen bonds       : angle       3.84935 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 203
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   40 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8864 (p)
REVERT: A   43 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7639 (pp20)
REVERT: A   45 TYR cc_start: 0.8114 (m-80) cc_final: 0.7635 (m-80)
REVERT: A   63 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9005 (mm)
REVERT: A  201 MET cc_start: 0.8588 (ttp) cc_final: 0.8331 (ttp)
REVERT: C   43 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7587 (pp20)
REVERT: C   45 TYR cc_start: 0.8110 (m-80) cc_final: 0.7596 (m-80)
REVERT: C   63 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9047 (mm)
REVERT: C  158 PHE cc_start: 0.9448 (OUTLIER) cc_final: 0.9176 (m-80)
REVERT: D   45 TYR cc_start: 0.8211 (m-80) cc_final: 0.7847 (m-80)
REVERT: D   63 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9038 (mm)
REVERT: D  158 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.9106 (m-80)
REVERT: E   40 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.8836 (p)
REVERT: E   43 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7518 (pp20)
REVERT: E   45 TYR cc_start: 0.8126 (m-80) cc_final: 0.7609 (m-80)
REVERT: E   63 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8967 (mm)
REVERT: E  154 MET cc_start: 0.8330 (tpt) cc_final: 0.8059 (tpt)
REVERT: E  158 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9123 (m-80)
  outliers start: 86
  outliers final: 69
  residues processed: 263
  average time/residue: 0.0625
  time to fit residues: 24.5564
Evaluate side-chains
  283 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 202
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain A residue   91 TRP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   91 TRP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   85 PHE
Chi-restraints excluded: chain D residue   91 TRP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain D residue  158 PHE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   26 THR
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 PHE
Chi-restraints excluded: chain E residue   91 TRP
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Chi-restraints excluded: chain E residue  228 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 80 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.117773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.092585 restraints weight = 15901.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.095743 restraints weight = 7216.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.097762 restraints weight = 4516.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.098856 restraints weight = 3433.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.099709 restraints weight = 2953.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   8244  Z= 0.236
  Angle     :  0.795  12.553  11112  Z= 0.391
  Chirality :  0.048   0.197   1260
  Planarity :  0.004   0.031   1272
  Dihedral  : 19.130 119.566   1524
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Rotamer:
    Outliers : 10.05 %
    Allowed  : 32.35 %
    Favored  : 57.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.29), residues: 896
  helix:  0.81 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -1.90 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 202 
 TYR   0.015   0.002   TYR A 159 
 PHE   0.020   0.002   PHE E  94 
 TRP   0.005   0.001   TRP C 212 
 HIS   0.002   0.001   HIS C 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 ( 8244)
  covalent geometry    : angle       0.79470 (11112)
  hydrogen bonds       : bond        0.04450 (  428)
  hydrogen bonds       : angle       4.10376 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 201
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A   40 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.8945 (p)
REVERT: A   43 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7567 (pp20)
REVERT: A   45 TYR cc_start: 0.8210 (m-80) cc_final: 0.7749 (m-80)
REVERT: A   63 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9056 (mm)
REVERT: A  194 GLU cc_start: 0.8478 (tp30) cc_final: 0.7919 (tm-30)
REVERT: C   40 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.8815 (p)
REVERT: C   43 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7577 (pp20)
REVERT: C   45 TYR cc_start: 0.8230 (m-80) cc_final: 0.7713 (m-80)
REVERT: C   63 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9068 (mm)
REVERT: C  158 PHE cc_start: 0.9461 (OUTLIER) cc_final: 0.9183 (m-80)
REVERT: C  194 GLU cc_start: 0.8422 (tp30) cc_final: 0.7878 (tm-30)
REVERT: D   45 TYR cc_start: 0.8334 (m-80) cc_final: 0.7992 (m-80)
REVERT: D   63 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9088 (mm)
REVERT: D  170 GLN cc_start: 0.8969 (tt0) cc_final: 0.8748 (tt0)
REVERT: E   40 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.8932 (p)
REVERT: E   43 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7484 (pp20)
REVERT: E   45 TYR cc_start: 0.8204 (m-80) cc_final: 0.7700 (m-80)
REVERT: E   63 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9052 (mm)
REVERT: E  154 MET cc_start: 0.8421 (tpt) cc_final: 0.8194 (tpt)
REVERT: E  158 PHE cc_start: 0.9462 (OUTLIER) cc_final: 0.9152 (m-80)
REVERT: E  194 GLU cc_start: 0.8413 (tp30) cc_final: 0.7843 (tm-30)
  outliers start: 82
  outliers final: 68
  residues processed: 259
  average time/residue: 0.0627
  time to fit residues: 24.3677
Evaluate side-chains
  278 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 198
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   91 TRP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   91 TRP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   26 THR
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   91 TRP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain D residue  228 ASN
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   26 THR
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   91 TRP
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Chi-restraints excluded: chain E residue  228 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 31 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.122439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.097369 restraints weight = 15312.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.100497 restraints weight = 6941.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.102553 restraints weight = 4311.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103719 restraints weight = 3262.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.104548 restraints weight = 2802.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8244  Z= 0.137
  Angle     :  0.740  12.326  11112  Z= 0.355
  Chirality :  0.045   0.187   1260
  Planarity :  0.003   0.031   1272
  Dihedral  : 17.903 112.162   1524
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers : 10.17 %
    Allowed  : 32.60 %
    Favored  : 57.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.29), residues: 896
  helix:  0.99 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.86 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 116 
 TYR   0.020   0.002   TYR A 159 
 PHE   0.020   0.001   PHE E  94 
 TRP   0.007   0.001   TRP A 196 
 HIS   0.001   0.000   HIS A  22 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8244)
  covalent geometry    : angle       0.73976 (11112)
  hydrogen bonds       : bond        0.03890 (  428)
  hydrogen bonds       : angle       3.81769 ( 1284)

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

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

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1792 Ramachandran restraints generated.
    896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 198
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   43 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7464 (pp20)
REVERT: A   63 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8964 (mm)
REVERT: A  220 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8589 (mt)
REVERT: C   40 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8767 (p)
REVERT: C   43 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7512 (pp20)
REVERT: C   63 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8954 (mm)
REVERT: C  158 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9059 (m-80)
REVERT: D   45 TYR cc_start: 0.8294 (m-80) cc_final: 0.7994 (m-80)
REVERT: D   63 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8990 (mm)
REVERT: D  158 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.9094 (m-80)
REVERT: E   40 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8794 (p)
REVERT: E   43 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7474 (pp20)
REVERT: E   45 TYR cc_start: 0.8136 (m-80) cc_final: 0.7655 (m-80)
REVERT: E   63 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8994 (mm)
REVERT: E  154 MET cc_start: 0.8264 (tpt) cc_final: 0.8024 (tpt)
REVERT: E  158 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.9046 (m-80)
REVERT: E  159 TYR cc_start: 0.8642 (t80) cc_final: 0.8371 (t80)
REVERT: E  220 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8575 (mt)
  outliers start: 83
  outliers final: 66
  residues processed: 259
  average time/residue: 0.0663
  time to fit residues: 25.7382
Evaluate side-chains
  271 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 191
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   85 PHE
Chi-restraints excluded: chain A residue   91 TRP
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  228 ASN
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   26 THR
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   43 GLU
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue   71 ILE
Chi-restraints excluded: chain C residue   85 PHE
Chi-restraints excluded: chain C residue   91 TRP
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  101 LEU
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  149 ASN
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain C residue  158 PHE
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain C residue  180 LEU
Chi-restraints excluded: chain C residue  187 LEU
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  220 LEU
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain D residue   19 ILE
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   71 ILE
Chi-restraints excluded: chain D residue   91 TRP
Chi-restraints excluded: chain D residue  100 SER
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  104 LEU
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  142 MET
Chi-restraints excluded: chain D residue  143 THR
Chi-restraints excluded: chain D residue  149 ASN
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain D residue  158 PHE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  187 LEU
Chi-restraints excluded: chain D residue  208 VAL
Chi-restraints excluded: chain D residue  220 LEU
Chi-restraints excluded: chain D residue  228 ASN
Chi-restraints excluded: chain E residue   19 ILE
Chi-restraints excluded: chain E residue   26 THR
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain E residue   43 GLU
Chi-restraints excluded: chain E residue   63 LEU
Chi-restraints excluded: chain E residue   71 ILE
Chi-restraints excluded: chain E residue   85 PHE
Chi-restraints excluded: chain E residue   91 TRP
Chi-restraints excluded: chain E residue  100 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  104 LEU
Chi-restraints excluded: chain E residue  118 LEU
Chi-restraints excluded: chain E residue  127 ILE
Chi-restraints excluded: chain E residue  143 THR
Chi-restraints excluded: chain E residue  149 ASN
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  158 PHE
Chi-restraints excluded: chain E residue  179 ASN
Chi-restraints excluded: chain E residue  180 LEU
Chi-restraints excluded: chain E residue  187 LEU
Chi-restraints excluded: chain E residue  208 VAL
Chi-restraints excluded: chain E residue  220 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 42 optimal weight:    0.8980
   chunk 74 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.119365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.094128 restraints weight = 15736.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.097324 restraints weight = 7145.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.099374 restraints weight = 4458.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100618 restraints weight = 3389.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.101117 restraints weight = 2902.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8244  Z= 0.191
  Angle     :  0.773  12.158  11112  Z= 0.378
  Chirality :  0.047   0.189   1260
  Planarity :  0.003   0.030   1272
  Dihedral  : 18.064 113.532   1524
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  9.80 %
    Allowed  : 33.58 %
    Favored  : 56.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.28), residues: 896
  helix:  0.93 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.86 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 116 
 TYR   0.011   0.002   TYR D 214 
 PHE   0.019   0.002   PHE E  94 
 TRP   0.004   0.001   TRP C 212 
 HIS   0.002   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 8244)
  covalent geometry    : angle       0.77262 (11112)
  hydrogen bonds       : bond        0.04151 (  428)
  hydrogen bonds       : angle       3.95379 ( 1284)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1368.50 seconds
wall clock time: 24 minutes 11.16 seconds (1451.16 seconds total)