Starting phenix.real_space_refine
on Sun Aug 24 07:06:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b0i_15784/08_2025/8b0i_15784.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b0i_15784/08_2025/8b0i_15784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b0i_15784/08_2025/8b0i_15784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b0i_15784/08_2025/8b0i_15784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b0i_15784/08_2025/8b0i_15784.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b0i_15784/08_2025/8b0i_15784.cif"
  }
  resolution = 4.28
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     103      5.49       5
     S      20      5.16       5
     C    5767      2.51       5
     N    1701      2.21       5
     O    2214      1.98       5
     H    7831      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17636
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 3560
          Classifications: {'peptide': 270}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 255}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 285
          Unresolved non-hydrogen angles: 354
          Unresolved non-hydrogen dihedrals: 237
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'ARG:plan': 15, 'TYR:plan': 2, 'GLU:plan': 8, 'ASP:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 180
    Chain: "B"
      Number of atoms: 3825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 3825
          Classifications: {'peptide': 281}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 265}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 276
          Unresolved non-hydrogen angles: 346
          Unresolved non-hydrogen dihedrals: 234
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'ARG:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'GLU:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 198
    Chain: "D"
      Number of atoms: 3763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 3763
          Classifications: {'peptide': 282}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 266}
          Unresolved non-hydrogen bonds: 275
          Unresolved non-hydrogen angles: 342
          Unresolved non-hydrogen dihedrals: 227
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'ARG:plan': 13, 'PHE:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 7, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 163
    Chain: "C"
      Number of atoms: 3298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 3298
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 14, 'TRANS': 227}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 211
          Unresolved non-hydrogen angles: 254
          Unresolved non-hydrogen dihedrals: 183
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'ARG:plan': 12, 'GLU:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 2, 'ASP:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 117
    Chain: "K"
      Number of atoms: 3190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 3190
          Classifications: {'RNA': 103}
          Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 27, 'rna3p_pur': 36, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 36, 'rna3p': 66}
          Chain breaks: 5
  Time building chain proxies: 2.98, per 1000 atoms: 0.17
  Number of scatterers: 17636
  At special positions: 0
  Unit cell: (93.888, 107.58, 142.788, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P     103     15.00
     O    2214      8.00
     N    1701      7.00
     C    5767      6.00
     H    7831      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 413.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2058

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 10 sheets defined
      49.2% alpha, 8.5% beta
      6 base pairs and 27 stacking pairs defined.
    Time for finding SS restraints: 2.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 24
    Processing helix  chain 'A' and resid 36 through 48
    Processing helix  chain 'A' and resid 63 through 74
    Processing helix  chain 'A' and resid 88 through 96
      removed outlier: 3.723A  pdb=" N   TYR A  96 " --> pdb=" O   LEU A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 129
      removed outlier: 3.939A  pdb=" N   GLU A 119 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      Proline residue:  A 125  - end of helix
    Processing helix  chain 'A' and resid 140 through 153
    Processing helix  chain 'A' and resid 188 through 192
      removed outlier: 3.762A  pdb=" N   TRP A 191 " --> pdb=" O   ASN A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 212
    Processing helix  chain 'A' and resid 212 through 235
      removed outlier: 3.728A  pdb=" N   HIS A 216 " --> pdb=" O   HIS A 212 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   TYR A 220 " --> pdb=" O   HIS A 216 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TRP A 229 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
      Proline residue:  A 231  - end of helix
      removed outlier: 3.962A  pdb=" N   THR A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 268
      removed outlier: 4.089A  pdb=" N   TYR A 256 " --> pdb=" O   HIS A 252 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ILE A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   TYR A 264 " --> pdb=" O   GLN A 260 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 281
      removed outlier: 3.977A  pdb=" N   LYS A 281 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 25
    Processing helix  chain 'B' and resid 36 through 41
      removed outlier: 3.859A  pdb=" N   LEU B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 47
    Processing helix  chain 'B' and resid 64 through 73
    Processing helix  chain 'B' and resid 88 through 99
    Processing helix  chain 'B' and resid 111 through 123
      removed outlier: 3.677A  pdb=" N   ASP B 121 " --> pdb=" O   ASP B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 129
    Processing helix  chain 'B' and resid 140 through 155
      removed outlier: 3.681A  pdb=" N   GLU B 146 " --> pdb=" O   HIS B 142 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   MET B 147 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS B 155 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 212
      removed outlier: 4.102A  pdb=" N   HIS B 212 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 235
      removed outlier: 3.919A  pdb=" N   TRP B 229 " --> pdb=" O   TYR B 225 " (cutoff:3.500A)
      Proline residue:  B 231  - end of helix
      removed outlier: 4.053A  pdb=" N   THR B 235 " --> pdb=" O   PRO B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 269
    Processing helix  chain 'D' and resid 13 through 25
      removed outlier: 4.157A  pdb=" N   ALA D  17 " --> pdb=" O   GLY D  13 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 35
      No H-bonds generated for 'chain 'D' and resid 33 through 35'
    Processing helix  chain 'D' and resid 36 through 46
      removed outlier: 4.142A  pdb=" N   ASP D  46 " --> pdb=" O   ARG D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 63 through 72
    Processing helix  chain 'D' and resid 88 through 99
    Processing helix  chain 'D' and resid 111 through 130
      removed outlier: 3.776A  pdb=" N   ALA D 115 " --> pdb=" O   SER D 111 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ILE D 116 " --> pdb=" O   LEU D 112 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   ASP D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ASP D 121 " --> pdb=" O   ASP D 117 " (cutoff:3.500A)
      Proline residue:  D 125  - end of helix
    Processing helix  chain 'D' and resid 140 through 148
      removed outlier: 3.820A  pdb=" N   ALA D 145 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   GLU D 146 " --> pdb=" O   HIS D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 149 through 151
      No H-bonds generated for 'chain 'D' and resid 149 through 151'
    Processing helix  chain 'D' and resid 188 through 192
    Processing helix  chain 'D' and resid 205 through 212
    Processing helix  chain 'D' and resid 212 through 228
      removed outlier: 3.668A  pdb=" N   LEU D 228 " --> pdb=" O   SER D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 229 through 235
      removed outlier: 3.737A  pdb=" N   THR D 235 " --> pdb=" O   PRO D 231 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 269
      removed outlier: 5.922A  pdb=" N   TYR D 256 " --> pdb=" O   HIS D 252 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ILE D 257 " --> pdb=" O   ARG D 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 14 through 25
      removed outlier: 3.621A  pdb=" N   GLU C  22 " --> pdb=" O   LEU C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 35 through 48
      removed outlier: 4.172A  pdb=" N   ASP C  39 " --> pdb=" O   VAL C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 74
    Processing helix  chain 'C' and resid 125 through 130
      removed outlier: 3.663A  pdb=" N   ARG C 129 " --> pdb=" O   PRO C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 145
    Processing helix  chain 'C' and resid 148 through 152
    Processing helix  chain 'C' and resid 188 through 192
    Processing helix  chain 'C' and resid 202 through 212
      removed outlier: 3.544A  pdb=" N   PHE C 208 " --> pdb=" O   PRO C 204 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG C 211 " --> pdb=" O   ALA C 207 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   HIS C 212 " --> pdb=" O   PHE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 235
      removed outlier: 3.708A  pdb=" N   HIS C 216 " --> pdb=" O   HIS C 212 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   TRP C 229 " --> pdb=" O   TYR C 225 " (cutoff:3.500A)
      Proline residue:  C 231  - end of helix
    Processing helix  chain 'C' and resid 251 through 269
      removed outlier: 4.497A  pdb=" N   TYR C 256 " --> pdb=" O   HIS C 252 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   ILE C 257 " --> pdb=" O   ARG C 253 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 281
      removed outlier: 4.259A  pdb=" N   LYS C 281 " --> pdb=" O   THR C 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 278 through 281'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7
      removed outlier: 6.997A  pdb=" N   LEU A   3 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU A  83 " --> pdb=" O   LEU A   3 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   ILE A   5 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU A 132 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 168
      removed outlier: 6.190A  pdb=" N   GLU A 165 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   CYS A 247 " --> pdb=" O   GLU A 165 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   PHE A 167 " --> pdb=" O   CYS A 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181
      removed outlier: 3.668A  pdb=" N   VAL A 180 " --> pdb=" O   VAL B 180 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL B 180 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   TYR B 179 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLY B 246 " --> pdb=" O   TYR B 179 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   PHE B 181 " --> pdb=" O   GLY B 246 " (cutoff:3.500A)
      removed outlier: 5.723A  pdb=" N   PHE B 167 " --> pdb=" O   CYS B 247 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.633A  pdb=" N   ASP B  86 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 163
      removed outlier: 5.583A  pdb=" N   THR B 161 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 5 through 6
      removed outlier: 6.755A  pdb=" N   ILE D   5 " --> pdb=" O   LEU D  83 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   LEU D  85 " --> pdb=" O   ILE D   5 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 30
      removed outlier: 5.493A  pdb=" N   TYR D  27 " --> pdb=" O   ALA D  52 " (cutoff:3.500A)
      removed outlier: 7.265A  pdb=" N   SER D  54 " --> pdb=" O   TYR D  27 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL D  29 " --> pdb=" O   SER D  54 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'D' and resid 272 through 274
      removed outlier: 3.537A  pdb=" N   ILE D 245 " --> pdb=" O   GLU D 165 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   TYR D 179 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   GLY D 246 " --> pdb=" O   TYR D 179 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   PHE D 181 " --> pdb=" O   GLY D 246 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL D 180 " --> pdb=" O   VAL C 180 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 30
      removed outlier: 6.678A  pdb=" N   TYR C  27 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 8.893A  pdb=" N   SER C  54 " --> pdb=" O   TYR C  27 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   VAL C  29 " --> pdb=" O   SER C  54 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 244 through 246
      removed outlier: 7.874A  pdb=" N   ILE C 245 " --> pdb=" O   VAL C 163 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   GLU C 165 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   MET C 162 " --> pdb=" O   GLN C 273 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   ARG C 275 " --> pdb=" O   MET C 162 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   PHE C 164 " --> pdb=" O   ARG C 275 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    314 hydrogen bonds defined for protein.
    912 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      13 hydrogen bonds
      22 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      27 stacking parallelities
  Total time for adding SS restraints: 3.00

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7379
        1.03 -     1.23: 791
        1.23 -     1.42: 4059
        1.42 -     1.62: 5727
        1.62 -     1.81: 64
  Bond restraints: 18020
  Sorted by residual:
  bond pdb=" N2    G K 115 "
       pdb=" H21   G K 115 "
    ideal  model  delta    sigma   weight residual
    0.860  1.049 -0.189 2.00e-02 2.50e+03 8.91e+01
  bond pdb=" N3    U K  32 "
       pdb=" H3    U K  32 "
    ideal  model  delta    sigma   weight residual
    0.860  1.040 -0.180 2.00e-02 2.50e+03 8.12e+01
  bond pdb=" N3    U K  70 "
       pdb=" H3    U K  70 "
    ideal  model  delta    sigma   weight residual
    0.860  1.040 -0.180 2.00e-02 2.50e+03 8.12e+01
  bond pdb=" N3    U K  69 "
       pdb=" H3    U K  69 "
    ideal  model  delta    sigma   weight residual
    0.860  1.040 -0.180 2.00e-02 2.50e+03 8.10e+01
  bond pdb=" N1    G K 135 "
       pdb=" H1    G K 135 "
    ideal  model  delta    sigma   weight residual
    0.860  1.040 -0.180 2.00e-02 2.50e+03 8.08e+01
  ... (remaining 18015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    21.76: 32283
       21.76 -    43.51: 5
       43.51 -    65.27: 0
       65.27 -    87.02: 0
       87.02 -   108.78: 5
  Bond angle restraints: 32293
  Sorted by residual:
  angle pdb=" H5'   G K  73 "
        pdb=" C5'   G K  73 "
        pdb="H5''   G K  73 "
      ideal   model   delta    sigma   weight residual
     109.00    0.22  108.78 3.00e+00 1.11e-01 1.31e+03
  angle pdb=" H5'   U K  84 "
        pdb=" C5'   U K  84 "
        pdb="H5''   U K  84 "
      ideal   model   delta    sigma   weight residual
     109.00    0.53  108.47 3.00e+00 1.11e-01 1.31e+03
  angle pdb=" H5'   A K  45 "
        pdb=" C5'   A K  45 "
        pdb="H5''   A K  45 "
      ideal   model   delta    sigma   weight residual
     109.00    0.85  108.15 3.00e+00 1.11e-01 1.30e+03
  angle pdb=" H5'   A K 129 "
        pdb=" C5'   A K 129 "
        pdb="H5''   A K 129 "
      ideal   model   delta    sigma   weight residual
     109.00    0.96  108.04 3.00e+00 1.11e-01 1.30e+03
  angle pdb=" O5'   G K 123 "
        pdb=" C5'   G K 123 "
        pdb="H5''   G K 123 "
      ideal   model   delta    sigma   weight residual
     109.00   21.92   87.08 3.00e+00 1.11e-01 8.43e+02
  ... (remaining 32288 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.99: 8128
       35.99 -    71.99: 566
       71.99 -   107.98: 117
      107.98 -   143.98: 5
      143.98 -   179.97: 37
  Dihedral angle restraints: 8853
    sinusoidal: 5343
      harmonic: 3510
  Sorted by residual:
  dihedral pdb=" O4'   U K 138 "
           pdb=" C1'   U K 138 "
           pdb=" N1    U K 138 "
           pdb=" C2    U K 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.52  156.48     1      1.50e+01 4.44e-03 8.18e+01
  dihedral pdb=" O4'   U K  84 "
           pdb=" C1'   U K  84 "
           pdb=" N1    U K  84 "
           pdb=" C2    U K  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.85  149.15     1      1.50e+01 4.44e-03 7.93e+01
  dihedral pdb=" O4'   C K  85 "
           pdb=" C1'   C K  85 "
           pdb=" N1    C K  85 "
           pdb=" C2    C K  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   51.23  148.77     1      1.50e+01 4.44e-03 7.92e+01
  ... (remaining 8850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.129: 1374
       0.129 -    0.257: 380
       0.257 -    0.386: 29
       0.386 -    0.514: 4
       0.514 -    0.643: 1
  Chirality restraints: 1788
  Sorted by residual:
  chirality pdb=" C3'   U K  36 "
            pdb=" C4'   U K  36 "
            pdb=" O3'   U K  36 "
            pdb=" C2'   U K  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.10   -0.64 2.00e-01 2.50e+01 1.03e+01
  chirality pdb=" C3'   G K  37 "
            pdb=" C4'   G K  37 "
            pdb=" O3'   G K  37 "
            pdb=" C2'   G K  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.24   -0.50 2.00e-01 2.50e+01 6.34e+00
  chirality pdb=" C3'   A K  53 "
            pdb=" C4'   A K  53 "
            pdb=" O3'   A K  53 "
            pdb=" C2'   A K  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.27   -0.47 2.00e-01 2.50e+01 5.56e+00
  ... (remaining 1785 not shown)

  Planarity restraints: 2593
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  59 "   -0.240 2.00e-02 2.50e+03   3.52e-01 1.86e+03
        pdb=" CG  ASN A  59 "    0.018 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  59 "    0.228 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  59 "    0.006 2.00e-02 2.50e+03
        pdb="HD21 ASN A  59 "   -0.569 2.00e-02 2.50e+03
        pdb="HD22 ASN A  59 "    0.557 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 271 "   -0.238 2.00e-02 2.50e+03   3.07e-01 1.41e+03
        pdb=" CG  ASN B 271 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 271 "    0.228 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 271 "    0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN B 271 "   -0.485 2.00e-02 2.50e+03
        pdb="HD22 ASN B 271 "    0.470 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN C  69 "   -0.191 2.00e-02 2.50e+03   2.22e-01 7.36e+02
        pdb=" CD  GLN C  69 "    0.013 2.00e-02 2.50e+03
        pdb=" OE1 GLN C  69 "    0.186 2.00e-02 2.50e+03
        pdb=" NE2 GLN C  69 "   -0.004 2.00e-02 2.50e+03
        pdb="HE21 GLN C  69 "    0.333 2.00e-02 2.50e+03
        pdb="HE22 GLN C  69 "   -0.336 2.00e-02 2.50e+03
  ... (remaining 2590 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 1155
        2.23 -     2.82: 34628
        2.82 -     3.42: 44190
        3.42 -     4.01: 55099
        4.01 -     4.60: 81309
  Nonbonded interactions: 216381
  Sorted by model distance:
  nonbonded pdb=" O   SER D 114 "
            pdb=" HG  SER D 114 "
     model   vdw
     1.640 2.450
  nonbonded pdb=" H3  MET A   1 "
            pdb=" O   ALA A  77 "
     model   vdw
     1.647 2.450
  nonbonded pdb=" O   TYR B  96 "
            pdb=" HG1 THR B  99 "
     model   vdw
     1.665 2.450
  nonbonded pdb=" O   GLN A 221 "
            pdb=" HG  SER A 224 "
     model   vdw
     1.696 2.450
  nonbonded pdb=" H8    A K  23 "
            pdb=" H2    A K  54 "
     model   vdw
     1.706 2.100
  ... (remaining 216376 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 2 or (resid 3 through 4 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or  \ 
(resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ 
e HA )) or resid 15 through 18 or (resid 19 and (name N or name CA or name C or  \ 
name O or name CB or name H or name HA )) or resid 20 through 21 or (resid 22 an \ 
d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ 
esid 23 or (resid 24 and (name N or name CA or name C or name O or name CB or na \ 
me H or name HA )) or resid 25 or (resid 26 through 29 and (name N or name CA or \ 
 name C or name O or name CB or name H or name HA )) or resid 30 or (resid 31 th \ 
rough 32 and (name N or name CA or name C or name O or name CB or name H or name \ 
 HA )) or resid 33 or (resid 34 and (name N or name CA or name C or name O or na \ 
me CB or name H or name HA )) or resid 35 or (resid 36 through 37 and (name N or \ 
 name CA or name C or name O or name CB or name H or name HA )) or resid 38 thro \ 
ugh 41 or (resid 42 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 43 or (resid 44 and (name N or name CA or name C or n \ 
ame O or name CB or name H or name HA )) or resid 45 or (resid 46 through 49 and \ 
 (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ 
sid 50 through 55 or (resid 56 and (name N or name CA or name C or name O or nam \ 
e CB or name H or name HA )) or resid 57 through 58 or (resid 59 through 60 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 61 or resid 63 through 65 or (resid 66 through 69 and (name N or name CA or n \ 
ame C or name O or name CB or name H or name HA )) or resid 70 through 73 or (re \ 
sid 74 and (name N or name CA or name C or name O or name CB or name H or name H \ 
A )) or resid 75 through 77 or (resid 78 and (name N or name CA or name C or nam \ 
e O or name CB or name H or name HA )) or resid 79 through 80 or (resid 81 throu \ 
gh 84 and (name N or name CA or name C or name O or name CB or name H or name HA \ 
 )) or resid 86 through 87 or (resid 88 through 91 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 92 or resid 124 throug \ 
h 128 or (resid 129 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 130 through 132 or (resid 133 and (name N or name CA  \ 
or name C or name O or name CB or name H or name HA )) or resid 134 through 141  \ 
or (resid 142 through 144 and (name N or name CA or name C or name O or name CB  \ 
or name H or name HA )) or resid 145 or resid 147 through 150 or (resid 151 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 152 through 156 or (resid 157 through 158 and (name N or name CA or name C or \ 
 name O or name CB or name H or name HA )) or resid 159 or (resid 160 and (name  \ 
N or name CA or name C or name O or name CB or name H or name HA )) or resid 161 \ 
 through 162 or (resid 163 through 165 and (name N or name CA or name C or name  \ 
O or name CB or name H or name HA )) or resid 166 or (resid 167 and (name N or n \ 
ame CA or name C or name O or name CB or name H or name HA )) or resid 168 throu \ 
gh 169 or (resid 170 and (name N or name CA or name C or name O or name CB or na \ 
me CG or name CD or name CE or name H or name HA or name HB2 or name HB3 or name \ 
 HG2 or name HG3 or name HD2 or name HD3)) or resid 171 through 172 or (resid 17 \ 
3 and (name N or name CA or name C or name O or name CB or name H or name HA ))  \ 
or resid 174 through 177 or (resid 178 and (name N or name CA or name C or name  \ 
O or name CB or name H or name HA )) or resid 179 through 181 or (resid 182 thro \ 
ugh 186 and (name N or name CA or name C or name O or name CB or name H or name  \ 
HA )) or resid 187 through 194 or (resid 195 through 196 and (name N or name CA  \ 
or name C or name O or name CB or name H or name HA )) or resid 197 through 200  \ 
or (resid 201 through 203 and (name N or name CA or name C or name O or name CB  \ 
or name H or name HA )) or resid 204 through 214 or (resid 215 and (name N or na \ 
me CA or name C or name O or name CB or name H or name HA )) or resid 216 throug \ 
h 217 or (resid 218 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 219 through 221 or (resid 222 through 223 and (name N \ 
 or name CA or name C or name O or name CB or name H or name HA )) or resid 224  \ 
through 227 or (resid 228 through 230 and (name N or name CA or name C or name O \ 
 or name CB or name H or name HA )) or resid 231 through 234 or (resid 235 throu \ 
gh 238 and (name N or name CA or name C or name O or name CB or name H or name H \ 
A )) or resid 239 through 240 or (resid 241 through 242 and (name N or name CA o \ 
r name C or name O or name CB or name H or name HA )) or resid 243 through 252 o \ 
r (resid 253 through 257 and (name N or name CA or name C or name O or name CB o \ 
r name H or name HA )) or resid 258 through 260 or (resid 261 and (name N or nam \ 
e CA or name C or name O or name CB or name H or name HA )) or resid 262 through \ 
 263 or (resid 264 and (name N or name CA or name C or name O or name CB or name \ 
 H or name HA )) or resid 265 or (resid 266 and (name N or name CA or name C or  \ 
name O or name CB or name H or name HA )) or resid 267 through 269 or (resid 270 \ 
 and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ 
r resid 271 through 275 or (resid 276 through 280 and (name N or name CA or name \ 
 C or name O or name CB or name H or name HA )) or resid 281 through 282))
  selection = (chain 'B' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or  \ 
(resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ 
e HA )) or resid 15 through 17 or (resid 18 through 19 and (name N or name CA or \ 
 name C or name O or name CB or name H or name HA )) or resid 20 or (resid 21 th \ 
rough 22 and (name N or name CA or name C or name O or name CB or name H or name \ 
 HA )) or resid 23 through 25 or (resid 26 through 29 and (name N or name CA or  \ 
name C or name O or name CB or name H or name HA )) or resid 30 through 48 or (r \ 
esid 49 and (name N or name CA or name C or name O or name CB or name H or name  \ 
HA )) or resid 50 through 64 or (resid 65 through 69 and (name N or name CA or n \ 
ame C or name O or name CB or name H or name HA )) or resid 70 through 73 or (re \ 
sid 74 and (name N or name CA or name C or name O or name CB or name H or name H \ 
A )) or resid 75 through 84 or (resid 86 and (name N or name CA or name C or nam \ 
e O or name CB or name H or name HA )) or resid 87 through 88 or (resid 89 throu \ 
gh 91 and (name N or name CA or name C or name O or name CB or name H or name HA \ 
 )) or resid 92 or (resid 124 and (name N or name CA or name C or name O or name \ 
 CB or name H or name HA )) or resid 125 or (resid 126 through 127 and (name N o \ 
r name CA or name C or name O or name CB or name H or name HA )) or resid 128 th \ 
rough 132 or (resid 133 and (name N or name CA or name C or name O or name CB or \ 
 name H or name HA )) or resid 134 through 135 or (resid 136 and (name N or name \ 
 CA or name C or name O or name CB or name H or name HA )) or resid 137 or (resi \ 
d 138 through 139 and (name N or name CA or name C or name O or name CB or name  \ 
H or name HA )) or resid 140 through 141 or (resid 142 through 144 and (name N o \ 
r name CA or name C or name O or name CB or name H or name HA )) or resid 145 or \ 
 resid 147 through 148 or (resid 149 and (name N or name CA or name C or name O  \ 
or name CB or name H or name HA )) or resid 150 or (resid 151 and (name N or nam \ 
e CA or name C or name O or name CB or name H or name HA )) or resid 152 or (res \ 
id 153 and (name N or name CA or name C or name O or name CB or name H or name H \ 
A )) or (resid 154 and (name N or name CA or name C or name O or name H )) or (r \ 
esid 155 through 158 and (name N or name CA or name C or name O or name CB or na \ 
me H or name HA )) or resid 159 or (resid 160 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 161 through 169 or (resid 1 \ 
70 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ 
r name CE or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 o \ 
r name HD2 or name HD3)) or resid 171 through 172 or (resid 173 and (name N or n \ 
ame CA or name C or name O or name CB or name H or name HA )) or resid 174 throu \ 
gh 181 or (resid 182 through 186 and (name N or name CA or name C or name O or n \ 
ame CB or name H or name HA )) or resid 187 or (resid 188 and (name N or name CA \ 
 or name C or name O or name CB or name H or name HA )) or resid 189 or (resid 1 \ 
90 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ 
 or resid 191 or (resid 192 and (name N or name CA or name C or name O or name C \ 
B or name H or name HA )) or resid 193 or (resid 194 through 196 and (name N or  \ 
name CA or name C or name O or name CB or name H or name HA )) or resid 197 or ( \ 
resid 198 through 199 and (name N or name CA or name C or name O or name CB or n \ 
ame H or name HA )) or resid 200 or (resid 201 through 203 and (name N or name C \ 
A or name C or name O or name CB or name H or name HA )) or resid 204 through 20 \ 
7 or (resid 208 and (name N or name CA or name C or name O or name CB or name H  \ 
or name HA )) or resid 209 through 210 or (resid 211 and (name N or name CA or n \ 
ame C or name O or name CB or name H or name HA )) or resid 212 through 213 or ( \ 
resid 214 through 215 and (name N or name CA or name C or name O or name CB or n \ 
ame H or name HA )) or resid 216 through 217 or (resid 218 and (name N or name C \ 
A or name C or name O or name CB or name H or name HA )) or resid 219 through 22 \ 
7 or (resid 228 through 230 and (name N or name CA or name C or name O or name C \ 
B or name H or name HA )) or resid 231 through 234 or (resid 235 through 238 and \ 
 (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ 
sid 239 through 240 or (resid 241 through 242 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 243 through 253 or (resid 2 \ 
54 through 257 and (name N or name CA or name C or name O or name CB or name H o \ 
r name HA )) or resid 258 through 259 or (resid 260 through 261 and (name N or n \ 
ame CA or name C or name O or name CB or name H or name HA )) or resid 262 throu \ 
gh 269 or (resid 270 and (name N or name CA or name C or name O or name CB or na \ 
me H or name HA )) or resid 271 through 274 or (resid 275 through 280 and (name  \ 
N or name CA or name C or name O or name CB or name H or name HA )) or resid 281 \ 
 through 282))
  selection = (chain 'C' and (resid 2 or (resid 3 through 4 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 5 through 17 or (resid 18 t \ 
hrough 19 and (name N or name CA or name C or name O or name CB or name H or nam \ 
e HA )) or resid 20 or (resid 21 through 22 and (name N or name CA or name C or  \ 
name O or name CB or name H or name HA )) or resid 23 through 25 or (resid 26 th \ 
rough 29 and (name N or name CA or name C or name O or name CB or name H or name \ 
 HA )) or resid 30 or (resid 31 through 32 and (name N or name CA or name C or n \ 
ame O or name CB or name H or name HA )) or resid 33 or (resid 34 and (name N or \ 
 name CA or name C or name O or name CB or name H or name HA )) or resid 35 thro \ 
ugh 36 or (resid 37 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 38 through 39 or (resid 40 and (name N or name CA or  \ 
name C or name O or name CB or name H or name HA )) or resid 41 or (resid 42 and \ 
 (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ 
sid 43 through 45 or (resid 46 through 49 and (name N or name CA or name C or na \ 
me O or name CB or name H or name HA )) or resid 50 through 55 or (resid 56 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 57 or (resid 58 through 60 and (name N or name CA or name C or name O or name \ 
 CB or name H or name HA )) or resid 61 or resid 63 through 65 or (resid 66 thro \ 
ugh 69 and (name N or name CA or name C or name O or name CB or name H or name H \ 
A )) or resid 70 through 73 or (resid 74 and (name N or name CA or name C or nam \ 
e O or name CB or name H or name HA )) or resid 75 through 77 or (resid 78 and ( \ 
name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ 
d 79 through 80 or (resid 81 through 86 and (name N or name CA or name C or name \ 
 O or name CB or name H or name HA )) or resid 87 or (resid 88 through 91 and (n \ 
ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 
 92 or (resid 124 and (name N or name CA or name C or name O or name CB or name  \ 
H or name HA )) or resid 125 or (resid 126 through 127 and (name N or name CA or \ 
 name C or name O or name CB or name H or name HA )) or resid 128 or (resid 129  \ 
and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ 
 resid 130 through 135 or (resid 136 and (name N or name CA or name C or name O  \ 
or name CB or name H or name HA )) or resid 137 through 142 or (resid 143 throug \ 
h 144 and (name N or name CA or name C or name O or name CB or name H or name HA \ 
 )) or resid 145 through 152 or (resid 153 and (name N or name CA or name C or n \ 
ame O or name CB or name H or name HA )) or resid 154 through 162 or (resid 163  \ 
through 165 and (name N or name CA or name C or name O or name CB or name H or n \ 
ame HA )) or resid 166 or (resid 167 and (name N or name CA or name C or name O  \ 
or name CB or name H or name HA )) or resid 168 through 177 or (resid 178 and (n \ 
ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 
 179 through 181 or (resid 182 through 186 and (name N or name CA or name C or n \ 
ame O or name CB or name H or name HA )) or resid 187 or (resid 188 and (name N  \ 
or name CA or name C or name O or name CB or name H or name HA )) or resid 189 o \ 
r (resid 190 and (name N or name CA or name C or name O or name CB or name H or  \ 
name HA )) or resid 191 or (resid 192 and (name N or name CA or name C or name O \ 
 or name CB or name H or name HA )) or resid 193 or (resid 194 through 196 and ( \ 
name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ 
d 197 through 198 or (resid 199 and (name N or name CA or name C or name O or na \ 
me CB or name H or name HA )) or resid 200 or (resid 201 through 203 and (name N \ 
 or name CA or name C or name O or name CB or name H or name HA )) or resid 204  \ 
through 207 or (resid 208 and (name N or name CA or name C or name O or name CB  \ 
or name H or name HA )) or resid 209 through 210 or (resid 211 and (name N or na \ 
me CA or name C or name O or name CB or name H or name HA )) or resid 212 throug \ 
h 213 or (resid 214 through 215 and (name N or name CA or name C or name O or na \ 
me CB or name H or name HA )) or resid 216 through 217 or (resid 218 and (name N \ 
 or name CA or name C or name O or name CB or name H or name HA )) or resid 219  \ 
through 220 or (resid 221 through 223 and (name N or name CA or name C or name O \ 
 or name CB or name H or name HA )) or resid 224 through 227 or (resid 228 throu \ 
gh 230 and (name N or name CA or name C or name O or name CB or name H or name H \ 
A )) or resid 231 or (resid 232 and (name N or name CA or name C or name O or na \ 
me CB or name H or name HA )) or resid 233 through 234 or (resid 235 through 238 \ 
 and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ 
r resid 239 through 254 or (resid 255 through 257 and (name N or name CA or name \ 
 C or name O or name CB or name H or name HA )) or resid 258 through 259 or (res \ 
id 260 through 261 and (name N or name CA or name C or name O or name CB or name \ 
 H or name HA )) or resid 262 through 263 or (resid 264 and (name N or name CA o \ 
r name C or name O or name CB or name H or name HA )) or resid 265 through 272 o \ 
r (resid 273 and (name N or name CA or name C or name O or name CB or name H or  \ 
name HA )) or resid 274 or (resid 275 through 280 and (name N or name CA or name \ 
 C or name O or name CB or name H or name HA )) or resid 281 through 282))
  selection = (chain 'D' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ 
r name O or name CB or name H or name HA )) or resid 5 through 6 or resid 13 or  \ 
(resid 14 and (name N or name CA or name C or name O or name CB or name H or nam \ 
e HA )) or resid 15 through 17 or (resid 18 through 19 and (name N or name CA or \ 
 name C or name O or name CB or name H or name HA )) or resid 20 or (resid 21 th \ 
rough 22 and (name N or name CA or name C or name O or name CB or name H or name \ 
 HA )) or resid 23 or (resid 24 and (name N or name CA or name C or name O or na \ 
me CB or name H or name HA )) or resid 25 through 30 or (resid 31 through 32 and \ 
 (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ 
sid 33 or (resid 34 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 35 or (resid 36 through 37 and (name N or name CA or  \ 
name C or name O or name CB or name H or name HA )) or resid 38 through 41 or (r \ 
esid 42 and (name N or name CA or name C or name O or name CB or name H or name  \ 
HA )) or resid 43 through 45 or (resid 46 through 49 and (name N or name CA or n \ 
ame C or name O or name CB or name H or name HA )) or resid 50 through 55 or (re \ 
sid 56 and (name N or name CA or name C or name O or name CB or name H or name H \ 
A )) or resid 57 or (resid 58 through 60 and (name N or name CA or name C or nam \ 
e O or name CB or name H or name HA )) or resid 61 or resid 63 through 66 or (re \ 
sid 67 through 69 and (name N or name CA or name C or name O or name CB or name  \ 
H or name HA )) or resid 70 through 77 or (resid 78 and (name N or name CA or na \ 
me C or name O or name CB or name H or name HA )) or resid 79 through 81 or (res \ 
id 82 through 84 and (name N or name CA or name C or name O or name CB or name H \ 
 or name HA )) or (resid 86 and (name N or name CA or name C or name O or name C \ 
B or name H or name HA )) or resid 87 or (resid 88 through 91 and (name N or nam \ 
e CA or name C or name O or name CB or name H or name HA )) or resid 92 or (resi \ 
d 124 and (name N or name CA or name C or name O or name CB or name H or name HA \ 
 )) or resid 125 through 126 or (resid 127 and (name N or name CA or name C or n \ 
ame O or name CB or name H or name HA )) or resid 128 through 132 or (resid 133  \ 
and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ 
 resid 134 through 135 or (resid 136 and (name N or name CA or name C or name O  \ 
or name CB or name H or name HA )) or resid 137 or (resid 138 through 139 and (n \ 
ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 
 140 through 141 or (resid 142 through 144 and (name N or name CA or name C or n \ 
ame O or name CB or name H or name HA )) or resid 145 or (resid 147 and (name N  \ 
or name CA or name C or name O or name CB or name H or name HA )) or resid 148 o \ 
r (resid 149 and (name N or name CA or name C or name O or name CB or name H or  \ 
name HA )) or resid 150 or (resid 151 and (name N or name CA or name C or name O \ 
 or name CB or name H or name HA )) or resid 152 through 157 or (resid 158 and ( \ 
name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ 
d 159 or (resid 160 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 161 or (resid 162 through 165 and (name N or name CA  \ 
or name C or name O or name CB or name H or name HA )) or resid 166 or (resid 16 \ 
7 and (name N or name CA or name C or name O or name CB or name H or name HA ))  \ 
or resid 168 through 169 or (resid 170 and (name N or name CA or name C or name  \ 
O or name CB or name CG or name CD or name CE or name H or name HA or name HB2 o \ 
r name HB3 or name HG2 or name HG3 or name HD2 or name HD3)) or resid 171 throug \ 
h 172 or (resid 173 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 174 through 177 or (resid 178 and (name N or name CA  \ 
or name C or name O or name CB or name H or name HA )) or resid 179 through 183  \ 
or (resid 184 through 186 and (name N or name CA or name C or name O or name CB  \ 
or name H or name HA )) or resid 187 or (resid 188 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 189 or (resid 190 and  \ 
(name N or name CA or name C or name O or name CB or name H or name HA )) or res \ 
id 191 or (resid 192 and (name N or name CA or name C or name O or name CB or na \ 
me H or name HA )) or resid 193 or (resid 194 through 196 and (name N or name CA \ 
 or name C or name O or name CB or name H or name HA )) or resid 197 or (resid 1 \ 
98 through 199 and (name N or name CA or name C or name O or name CB or name H o \ 
r name HA )) or resid 200 through 220 or (resid 221 through 223 and (name N or n \ 
ame CA or name C or name O or name CB or name H or name HA )) or resid 224 throu \ 
gh 228 or (resid 229 through 230 and (name N or name CA or name C or name O or n \ 
ame CB or name H or name HA )) or resid 231 through 235 or (resid 236 through 23 \ 
8 and (name N or name CA or name C or name O or name CB or name H or name HA ))  \ 
or resid 239 through 240 or (resid 241 through 242 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 243 through 246 or (re \ 
sid 247 and (name N or name CA or name C or name O or name CB or name H or name  \ 
HA )) or resid 248 through 251 or (resid 252 through 257 and (name N or name CA  \ 
or name C or name O or name CB or name H or name HA )) or resid 258 through 259  \ 
or (resid 260 through 261 and (name N or name CA or name C or name O or name CB  \ 
or name H or name HA )) or resid 262 through 263 or (resid 264 and (name N or na \ 
me CA or name C or name O or name CB or name H or name HA )) or resid 265 throug \ 
h 267 or (resid 268 and (name N or name CA or name C or name O or name CB or nam \ 
e H or name HA )) or resid 269 or (resid 270 and (name N or name CA or name C or \ 
 name O or name CB or name H or name HA )) or resid 271 through 272 or (resid 27 \ 
3 and (name N or name CA or name C or name O or name CB or name H or name HA ))  \ 
or resid 274 through 275 or (resid 276 through 280 and (name N or name CA or nam \ 
e C or name O or name CB or name H or name HA )) or resid 281 through 282))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.470
  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:             0.080
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     15.140
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
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   0.087  10189  Z= 0.893
  Angle     :  1.979  13.684  14374  Z= 1.480
  Chirality :  0.108   0.643   1788
  Planarity :  0.011   0.076   1512
  Dihedral  : 24.774 179.381   4228
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  6.17 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.10 %
  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 aren not related in a simple way.
  whole: -1.62 (0.25), residues: 1055
  helix: -0.52 (0.24), residues: 431
  sheet: -1.70 (0.37), residues: 175
  loop : -1.20 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  89 
 TYR   0.042   0.004   TYR A 256 
 PHE   0.034   0.003   PHE B 218 
 TRP   0.037   0.004   TRP B 229 
 HIS   0.013   0.003   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.01203 (10189)
  covalent geometry    : angle       1.97931 (14374)
  hydrogen bonds       : bond        0.25338 (  327)
  hydrogen bonds       : angle      11.08099 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  418 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 417
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLN cc_start: 0.9685 (tt0) cc_final: 0.9295 (tp-100)
REVERT: A   73 ASN cc_start: 0.8993 (m-40) cc_final: 0.8282 (m-40)
REVERT: A  112 LEU cc_start: 0.9174 (mp) cc_final: 0.8862 (tp)
REVERT: A  210 ASP cc_start: 0.9403 (p0) cc_final: 0.9149 (p0)
REVERT: A  212 HIS cc_start: 0.8830 (m-70) cc_final: 0.8205 (m-70)
REVERT: A  266 ARG cc_start: 0.9490 (tpp-160) cc_final: 0.9229 (ttm-80)
REVERT: A  276 HIS cc_start: 0.8602 (p-80) cc_final: 0.8372 (p-80)
REVERT: B   91 THR cc_start: 0.9541 (m) cc_final: 0.9059 (t)
REVERT: B   98 ASP cc_start: 0.9350 (m-30) cc_final: 0.9037 (m-30)
REVERT: B  112 LEU cc_start: 0.9524 (tp) cc_final: 0.9261 (tp)
REVERT: B  148 LEU cc_start: 0.9560 (mt) cc_final: 0.9239 (mt)
REVERT: B  171 HIS cc_start: 0.8851 (m-70) cc_final: 0.8376 (t-90)
REVERT: B  186 LEU cc_start: 0.8875 (mt) cc_final: 0.8640 (mt)
REVERT: D  107 SER cc_start: 0.9733 (t) cc_final: 0.9447 (p)
REVERT: D  149 ARG cc_start: 0.9478 (tpp-160) cc_final: 0.8990 (tpt90)
REVERT: D  263 ASP cc_start: 0.9008 (m-30) cc_final: 0.8763 (m-30)
REVERT: C  212 HIS cc_start: 0.8669 (m-70) cc_final: 0.8413 (m90)
  outliers start: 1
  outliers final: 1
  residues processed: 417
  average time/residue: 0.2053
  time to fit residues: 113.3169
Evaluate side-chains
  306 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 305
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 212 HIS

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 = 0.090013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.067344 restraints weight = 120012.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.070409 restraints weight = 67952.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.072692 restraints weight = 45028.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.074313 restraints weight = 33207.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.075427 restraints weight = 26547.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3469 r_free = 0.3469    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10189  Z= 0.152
  Angle     :  0.707   7.795  14374  Z= 0.374
  Chirality :  0.042   0.227   1788
  Planarity :  0.005   0.081   1512
  Dihedral  : 27.523 176.796   2716
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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 aren not related in a simple way.
  whole: -0.94 (0.26), residues: 1055
  helix:  0.14 (0.23), residues: 457
  sheet: -1.53 (0.33), residues: 209
  loop : -0.78 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 149 
 TYR   0.011   0.001   TYR B 220 
 PHE   0.015   0.001   PHE D  67 
 TRP   0.013   0.002   TRP B 229 
 HIS   0.005   0.001   HIS D 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10189)
  covalent geometry    : angle       0.70706 (14374)
  hydrogen bonds       : bond        0.05631 (  327)
  hydrogen bonds       : angle       6.66304 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  364 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 364
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLN cc_start: 0.9784 (tt0) cc_final: 0.9525 (tp-100)
REVERT: A  112 LEU cc_start: 0.8869 (mp) cc_final: 0.8438 (tp)
REVERT: A  146 GLU cc_start: 0.9379 (tp30) cc_final: 0.8833 (tp30)
REVERT: A  178 ASP cc_start: 0.9065 (m-30) cc_final: 0.8863 (p0)
REVERT: A  191 TRP cc_start: 0.9297 (m-10) cc_final: 0.8784 (m-10)
REVERT: A  265 PHE cc_start: 0.9623 (m-80) cc_final: 0.9263 (m-80)
REVERT: A  266 ARG cc_start: 0.9465 (tpp-160) cc_final: 0.9058 (ttm-80)
REVERT: A  272 VAL cc_start: 0.6896 (p) cc_final: 0.6260 (p)
REVERT: A  276 HIS cc_start: 0.8826 (p-80) cc_final: 0.8526 (p-80)
REVERT: B   26 PHE cc_start: 0.9371 (m-80) cc_final: 0.9052 (m-10)
REVERT: B   91 THR cc_start: 0.9301 (m) cc_final: 0.8901 (t)
REVERT: B   98 ASP cc_start: 0.9270 (m-30) cc_final: 0.9016 (m-30)
REVERT: B  112 LEU cc_start: 0.9427 (tp) cc_final: 0.9215 (tp)
REVERT: B  171 HIS cc_start: 0.8803 (m-70) cc_final: 0.8150 (t-90)
REVERT: B  220 TYR cc_start: 0.9023 (m-80) cc_final: 0.8640 (m-80)
REVERT: B  271 ASN cc_start: 0.9498 (t0) cc_final: 0.8968 (t0)
REVERT: D  113 GLU cc_start: 0.9092 (tp30) cc_final: 0.8848 (tp30)
REVERT: D  149 ARG cc_start: 0.9643 (tpp-160) cc_final: 0.9004 (tpt90)
REVERT: D  169 PHE cc_start: 0.8139 (m-80) cc_final: 0.7720 (m-80)
REVERT: D  220 TYR cc_start: 0.9382 (t80) cc_final: 0.8916 (t80)
REVERT: C  227 GLU cc_start: 0.9633 (tp30) cc_final: 0.9405 (tp30)
REVERT: C  230 LEU cc_start: 0.9686 (tp) cc_final: 0.9438 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 364
  average time/residue: 0.2133
  time to fit residues: 101.0654
Evaluate side-chains
  290 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 31 optimal weight:    0.5980
   chunk 9 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 55 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 82 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 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 = 0.3695 r_free = 0.3695 target = 0.087529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.065278 restraints weight = 128554.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.068104 restraints weight = 73422.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.070195 restraints weight = 49454.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.071652 restraints weight = 36911.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.072732 restraints weight = 29854.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3394 r_free = 0.3394    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10189  Z= 0.140
  Angle     :  0.606   6.909  14374  Z= 0.325
  Chirality :  0.039   0.196   1788
  Planarity :  0.004   0.068   1512
  Dihedral  : 27.152 178.770   2716
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  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 aren not related in a simple way.
  whole: -0.40 (0.26), residues: 1055
  helix:  0.58 (0.24), residues: 472
  sheet: -1.24 (0.33), residues: 205
  loop : -0.57 (0.34), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  89 
 TYR   0.010   0.001   TYR C 256 
 PHE   0.011   0.001   PHE C 218 
 TRP   0.010   0.001   TRP B 229 
 HIS   0.005   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10189)
  covalent geometry    : angle       0.60583 (14374)
  hydrogen bonds       : bond        0.04647 (  327)
  hydrogen bonds       : angle       5.93249 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  349 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 349
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 ILE cc_start: 0.9048 (mm) cc_final: 0.8705 (mm)
REVERT: A   69 GLN cc_start: 0.9802 (tt0) cc_final: 0.9553 (tp-100)
REVERT: A   85 LEU cc_start: 0.9591 (mp) cc_final: 0.9091 (tt)
REVERT: A  112 LEU cc_start: 0.8879 (mp) cc_final: 0.8408 (tp)
REVERT: A  146 GLU cc_start: 0.9418 (tp30) cc_final: 0.8944 (tp30)
REVERT: A  178 ASP cc_start: 0.9207 (m-30) cc_final: 0.8811 (p0)
REVERT: A  191 TRP cc_start: 0.9283 (m-10) cc_final: 0.8989 (m-10)
REVERT: A  265 PHE cc_start: 0.9661 (m-80) cc_final: 0.9314 (m-80)
REVERT: A  266 ARG cc_start: 0.9532 (tpp-160) cc_final: 0.9295 (ttm-80)
REVERT: A  276 HIS cc_start: 0.8784 (p-80) cc_final: 0.8475 (p-80)
REVERT: B   18 LEU cc_start: 0.9488 (tp) cc_final: 0.9286 (tp)
REVERT: B   22 GLU cc_start: 0.9563 (pt0) cc_final: 0.9313 (pt0)
REVERT: B   91 THR cc_start: 0.9295 (m) cc_final: 0.8894 (t)
REVERT: B   98 ASP cc_start: 0.9306 (m-30) cc_final: 0.9062 (m-30)
REVERT: B  112 LEU cc_start: 0.9439 (tp) cc_final: 0.9223 (tp)
REVERT: B  136 THR cc_start: 0.9069 (p) cc_final: 0.8860 (p)
REVERT: B  171 HIS cc_start: 0.8967 (m-70) cc_final: 0.8330 (t-90)
REVERT: B  220 TYR cc_start: 0.9035 (m-80) cc_final: 0.8623 (m-80)
REVERT: B  271 ASN cc_start: 0.9373 (t0) cc_final: 0.8936 (t0)
REVERT: D   18 LEU cc_start: 0.9573 (tp) cc_final: 0.9342 (tp)
REVERT: D   39 ASP cc_start: 0.9492 (m-30) cc_final: 0.9175 (p0)
REVERT: D   94 ARG cc_start: 0.9450 (ttp80) cc_final: 0.9177 (tpp80)
REVERT: D  149 ARG cc_start: 0.9679 (tpp-160) cc_final: 0.8984 (tpt90)
REVERT: D  224 SER cc_start: 0.9479 (m) cc_final: 0.9181 (p)
REVERT: C  165 GLU cc_start: 0.8437 (mp0) cc_final: 0.8209 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 349
  average time/residue: 0.2069
  time to fit residues: 95.6276
Evaluate side-chains
  304 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 304
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 112 optimal weight:   10.0000
   chunk 46 optimal weight:    7.9990
   chunk 115 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 260 GLN
D 171 HIS
D 217 ASN
C  73 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.084338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.062539 restraints weight = 132899.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.065224 restraints weight = 76052.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.067236 restraints weight = 51142.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.068696 restraints weight = 38172.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.069691 restraints weight = 30838.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3333
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3333 r_free = 0.3333    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
r_final: 0.3333
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.5874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10189  Z= 0.183
  Angle     :  0.619   7.367  14374  Z= 0.329
  Chirality :  0.038   0.201   1788
  Planarity :  0.004   0.066   1512
  Dihedral  : 27.127 179.766   2716
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  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 aren not related in a simple way.
  whole: -0.41 (0.26), residues: 1055
  helix:  0.49 (0.24), residues: 467
  sheet: -1.06 (0.34), residues: 198
  loop : -0.58 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  89 
 TYR   0.011   0.002   TYR D 179 
 PHE   0.019   0.001   PHE D  84 
 TRP   0.011   0.001   TRP B 229 
 HIS   0.004   0.001   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10189)
  covalent geometry    : angle       0.61891 (14374)
  hydrogen bonds       : bond        0.04504 (  327)
  hydrogen bonds       : angle       5.86050 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  319 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 319
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 CYS cc_start: 0.8592 (p) cc_final: 0.8213 (p)
REVERT: A   69 GLN cc_start: 0.9814 (tt0) cc_final: 0.9587 (tp-100)
REVERT: A  146 GLU cc_start: 0.9442 (tp30) cc_final: 0.9005 (tp30)
REVERT: A  264 TYR cc_start: 0.9468 (t80) cc_final: 0.9213 (t80)
REVERT: A  265 PHE cc_start: 0.9725 (m-80) cc_final: 0.9430 (m-80)
REVERT: A  266 ARG cc_start: 0.9571 (tpp-160) cc_final: 0.9308 (ttm-80)
REVERT: B   18 LEU cc_start: 0.9562 (tp) cc_final: 0.9247 (tp)
REVERT: B   22 GLU cc_start: 0.9566 (pt0) cc_final: 0.9308 (pt0)
REVERT: B   98 ASP cc_start: 0.9335 (m-30) cc_final: 0.9090 (m-30)
REVERT: B  146 GLU cc_start: 0.9046 (mp0) cc_final: 0.8757 (mp0)
REVERT: B  171 HIS cc_start: 0.9102 (m-70) cc_final: 0.8397 (t-90)
REVERT: B  220 TYR cc_start: 0.9053 (m-80) cc_final: 0.8643 (m-80)
REVERT: B  230 LEU cc_start: 0.9727 (tp) cc_final: 0.9525 (tp)
REVERT: D  149 ARG cc_start: 0.9644 (tpp-160) cc_final: 0.8985 (tpt90)
REVERT: D  220 TYR cc_start: 0.9352 (t80) cc_final: 0.8914 (t80)
REVERT: C   71 MET cc_start: 0.9116 (mmp) cc_final: 0.8873 (mmm)
REVERT: C  169 PHE cc_start: 0.8869 (m-80) cc_final: 0.8486 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 319
  average time/residue: 0.2017
  time to fit residues: 85.6735
Evaluate side-chains
  271 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 80 optimal weight:   10.0000
   chunk 116 optimal weight:    6.9990
   chunk 103 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   chunk 83 optimal weight:    9.9990
   chunk 59 optimal weight:    0.3980
   chunk 25 optimal weight:    4.9990
   chunk 113 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    3.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 HIS
C  69 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.080010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.058508 restraints weight = 139164.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.061026 restraints weight = 79845.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.062869 restraints weight = 54235.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.064181 restraints weight = 41109.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.064965 restraints weight = 33752.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.6786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  10189  Z= 0.257
  Angle     :  0.687   7.274  14374  Z= 0.371
  Chirality :  0.040   0.221   1788
  Planarity :  0.005   0.061   1512
  Dihedral  : 27.228 178.278   2716
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  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 aren not related in a simple way.
  whole: -1.06 (0.26), residues: 1055
  helix: -0.23 (0.23), residues: 465
  sheet: -1.35 (0.36), residues: 193
  loop : -0.69 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  94 
 TYR   0.022   0.002   TYR C 225 
 PHE   0.016   0.002   PHE C 181 
 TRP   0.014   0.002   TRP B 229 
 HIS   0.008   0.002   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (10189)
  covalent geometry    : angle       0.68706 (14374)
  hydrogen bonds       : bond        0.04963 (  327)
  hydrogen bonds       : angle       6.34879 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  289 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLN cc_start: 0.9830 (tt0) cc_final: 0.9624 (tp-100)
REVERT: A  146 GLU cc_start: 0.9494 (tp30) cc_final: 0.9085 (tp30)
REVERT: A  178 ASP cc_start: 0.8916 (p0) cc_final: 0.8342 (p0)
REVERT: A  264 TYR cc_start: 0.9450 (t80) cc_final: 0.9136 (t80)
REVERT: A  266 ARG cc_start: 0.9613 (tpp-160) cc_final: 0.9366 (ttm-80)
REVERT: B   18 LEU cc_start: 0.9605 (tp) cc_final: 0.9304 (tp)
REVERT: B   22 GLU cc_start: 0.9593 (pt0) cc_final: 0.9323 (pt0)
REVERT: B   26 PHE cc_start: 0.9381 (m-80) cc_final: 0.8906 (m-80)
REVERT: B  171 HIS cc_start: 0.9275 (m-70) cc_final: 0.8509 (t70)
REVERT: B  186 LEU cc_start: 0.9188 (mt) cc_final: 0.8946 (mt)
REVERT: B  220 TYR cc_start: 0.9084 (m-80) cc_final: 0.8646 (m-80)
REVERT: B  259 GLU cc_start: 0.9349 (tm-30) cc_final: 0.9128 (tm-30)
REVERT: D   39 ASP cc_start: 0.9522 (m-30) cc_final: 0.9096 (p0)
REVERT: D  138 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7564 (mt-10)
REVERT: D  149 ARG cc_start: 0.9648 (tpp-160) cc_final: 0.9221 (mmm160)
REVERT: D  162 MET cc_start: 0.9201 (pmm) cc_final: 0.8952 (pmm)
REVERT: D  178 ASP cc_start: 0.7793 (m-30) cc_final: 0.7350 (m-30)
REVERT: D  220 TYR cc_start: 0.9285 (t80) cc_final: 0.8837 (t80)
REVERT: D  242 THR cc_start: 0.7621 (p) cc_final: 0.6962 (p)
REVERT: C   71 MET cc_start: 0.9230 (mmp) cc_final: 0.8990 (mmm)
REVERT: C  165 GLU cc_start: 0.8759 (mp0) cc_final: 0.8520 (mp0)
REVERT: C  169 PHE cc_start: 0.8916 (m-80) cc_final: 0.8702 (m-80)
REVERT: C  259 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8893 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.2104
  time to fit residues: 79.8588
Evaluate side-chains
  267 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 267
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 107 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 70 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 115 optimal weight:    7.9990
   chunk 35 optimal weight:   10.0000
   chunk 54 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 114 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 HIS
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.075986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.055859 restraints weight = 149054.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.058172 restraints weight = 86244.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.059818 restraints weight = 59285.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.060991 restraints weight = 45560.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.061642 restraints weight = 37832.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.7862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073  10189  Z= 0.406
  Angle     :  0.880   7.403  14374  Z= 0.480
  Chirality :  0.045   0.249   1788
  Planarity :  0.007   0.058   1512
  Dihedral  : 27.705 177.065   2716
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 36.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.05 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  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 aren not related in a simple way.
  whole: -2.63 (0.24), residues: 1055
  helix: -1.54 (0.21), residues: 467
  sheet: -2.12 (0.36), residues: 169
  loop : -1.55 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 151 
 TYR   0.032   0.003   TYR A 179 
 PHE   0.026   0.003   PHE C 181 
 TRP   0.022   0.003   TRP D 229 
 HIS   0.015   0.003   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00738 (10189)
  covalent geometry    : angle       0.87951 (14374)
  hydrogen bonds       : bond        0.06703 (  327)
  hydrogen bonds       : angle       7.32803 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  268 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9431 (mm-30)
REVERT: A   69 GLN cc_start: 0.9816 (tt0) cc_final: 0.9610 (tp-100)
REVERT: A  266 ARG cc_start: 0.9628 (tpp-160) cc_final: 0.9377 (ttm-80)
REVERT: B   18 LEU cc_start: 0.9672 (tp) cc_final: 0.9371 (tp)
REVERT: B   22 GLU cc_start: 0.9585 (pt0) cc_final: 0.9354 (pt0)
REVERT: B   26 PHE cc_start: 0.9326 (m-80) cc_final: 0.8707 (m-80)
REVERT: B  155 LYS cc_start: 0.8446 (pptt) cc_final: 0.8128 (ptmm)
REVERT: B  171 HIS cc_start: 0.9391 (m-70) cc_final: 0.9106 (m-70)
REVERT: B  259 GLU cc_start: 0.9330 (tm-30) cc_final: 0.9119 (tm-30)
REVERT: D  178 ASP cc_start: 0.7761 (m-30) cc_final: 0.7358 (m-30)
REVERT: D  220 TYR cc_start: 0.9210 (t80) cc_final: 0.8789 (t80)
REVERT: D  242 THR cc_start: 0.7608 (p) cc_final: 0.6954 (p)
REVERT: C   26 PHE cc_start: 0.9203 (m-80) cc_final: 0.8925 (m-80)
REVERT: C   58 ARG cc_start: 0.8555 (ttt180) cc_final: 0.8311 (ttt180)
REVERT: C   71 MET cc_start: 0.9327 (mmp) cc_final: 0.9112 (mmm)
REVERT: C  265 PHE cc_start: 0.9822 (m-80) cc_final: 0.9458 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1917
  time to fit residues: 67.9931
Evaluate side-chains
  243 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 110 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  59 ASN
** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 276 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.080773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.059245 restraints weight = 140142.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.061887 restraints weight = 79224.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.063816 restraints weight = 53640.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.065234 restraints weight = 40585.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.066143 restraints weight = 33289.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.7904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10189  Z= 0.134
  Angle     :  0.592   7.166  14374  Z= 0.314
  Chirality :  0.039   0.195   1788
  Planarity :  0.005   0.062   1512
  Dihedral  : 26.994 179.180   2716
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  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 aren not related in a simple way.
  whole: -1.31 (0.26), residues: 1055
  helix: -0.20 (0.23), residues: 469
  sheet: -1.96 (0.35), residues: 189
  loop : -0.87 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 101 
 TYR   0.014   0.002   TYR A 220 
 PHE   0.011   0.001   PHE C 265 
 TRP   0.013   0.001   TRP B 229 
 HIS   0.005   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10189)
  covalent geometry    : angle       0.59248 (14374)
  hydrogen bonds       : bond        0.04286 (  327)
  hydrogen bonds       : angle       6.03377 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  290 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.9608 (mm-30) cc_final: 0.9379 (mm-30)
REVERT: A  146 GLU cc_start: 0.9587 (tp30) cc_final: 0.9234 (tp30)
REVERT: A  266 ARG cc_start: 0.9629 (tpp-160) cc_final: 0.9310 (ttm-80)
REVERT: B    4 MET cc_start: 0.9447 (mmm) cc_final: 0.9127 (tpp)
REVERT: B   18 LEU cc_start: 0.9616 (tp) cc_final: 0.9320 (tp)
REVERT: B   22 GLU cc_start: 0.9592 (pt0) cc_final: 0.9340 (pt0)
REVERT: B   26 PHE cc_start: 0.9338 (m-80) cc_final: 0.8797 (m-80)
REVERT: B  171 HIS cc_start: 0.9373 (m-70) cc_final: 0.9062 (m-70)
REVERT: B  186 LEU cc_start: 0.9205 (mt) cc_final: 0.8961 (mt)
REVERT: D   39 ASP cc_start: 0.9499 (m-30) cc_final: 0.9049 (p0)
REVERT: D  162 MET cc_start: 0.9260 (pmm) cc_final: 0.9006 (pmm)
REVERT: D  178 ASP cc_start: 0.7676 (m-30) cc_final: 0.7293 (m-30)
REVERT: D  220 TYR cc_start: 0.9231 (t80) cc_final: 0.8784 (t80)
REVERT: D  242 THR cc_start: 0.7537 (p) cc_final: 0.6966 (p)
REVERT: C   71 MET cc_start: 0.9207 (mmp) cc_final: 0.8973 (mmm)
REVERT: C  165 GLU cc_start: 0.8836 (mp0) cc_final: 0.8450 (mp0)
REVERT: C  265 PHE cc_start: 0.9743 (m-80) cc_final: 0.9427 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1897
  time to fit residues: 73.8930
Evaluate side-chains
  252 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 110 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A  73 ASN
** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.078872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.057719 restraints weight = 130296.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.060251 restraints weight = 73825.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.062138 restraints weight = 49822.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.063464 restraints weight = 37532.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.064395 restraints weight = 30564.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.8143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10189  Z= 0.189
  Angle     :  0.611   6.854  14374  Z= 0.326
  Chirality :  0.038   0.198   1788
  Planarity :  0.005   0.061   1512
  Dihedral  : 26.990 179.434   2716
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.26), residues: 1055
  helix: -0.08 (0.24), residues: 475
  sheet: -1.96 (0.36), residues: 189
  loop : -0.83 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 101 
 TYR   0.013   0.002   TYR B 225 
 PHE   0.012   0.001   PHE C 218 
 TRP   0.012   0.001   TRP B 229 
 HIS   0.006   0.001   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (10189)
  covalent geometry    : angle       0.61068 (14374)
  hydrogen bonds       : bond        0.04495 (  327)
  hydrogen bonds       : angle       6.05391 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  280 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 GLU cc_start: 0.9580 (tp30) cc_final: 0.9197 (tp30)
REVERT: A  266 ARG cc_start: 0.9637 (tpp-160) cc_final: 0.9250 (ttm-80)
REVERT: B    4 MET cc_start: 0.9418 (mmm) cc_final: 0.9132 (tpp)
REVERT: B   18 LEU cc_start: 0.9636 (tp) cc_final: 0.9331 (tp)
REVERT: B   22 GLU cc_start: 0.9587 (pt0) cc_final: 0.9354 (pt0)
REVERT: B   26 PHE cc_start: 0.9363 (m-80) cc_final: 0.8822 (m-80)
REVERT: B   28 CYS cc_start: 0.9244 (p) cc_final: 0.8864 (p)
REVERT: B  171 HIS cc_start: 0.9383 (m-70) cc_final: 0.9059 (m-70)
REVERT: D   39 ASP cc_start: 0.9510 (m-30) cc_final: 0.9076 (p0)
REVERT: D  178 ASP cc_start: 0.7702 (m-30) cc_final: 0.7407 (m-30)
REVERT: D  220 TYR cc_start: 0.9260 (t80) cc_final: 0.8824 (t80)
REVERT: D  242 THR cc_start: 0.7527 (p) cc_final: 0.6947 (p)
REVERT: C   58 ARG cc_start: 0.8523 (ttt180) cc_final: 0.7939 (mtt90)
REVERT: C   71 MET cc_start: 0.9209 (mmp) cc_final: 0.8981 (mmm)
REVERT: C  165 GLU cc_start: 0.8747 (mp0) cc_final: 0.8291 (mp0)
REVERT: C  265 PHE cc_start: 0.9746 (m-80) cc_final: 0.9446 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1927
  time to fit residues: 73.0547
Evaluate side-chains
  255 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 90 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.079181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.057515 restraints weight = 134512.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.060058 restraints weight = 76156.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.061897 restraints weight = 51497.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.063004 restraints weight = 39041.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.063998 restraints weight = 32790.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.8337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10189  Z= 0.164
  Angle     :  0.587   6.760  14374  Z= 0.312
  Chirality :  0.038   0.195   1788
  Planarity :  0.005   0.062   1512
  Dihedral  : 26.836 179.155   2716
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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 aren not related in a simple way.
  whole: -0.97 (0.27), residues: 1055
  helix:  0.14 (0.24), residues: 469
  sheet: -1.86 (0.36), residues: 189
  loop : -0.74 (0.34), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 101 
 TYR   0.013   0.001   TYR C 225 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.012   0.001   TRP B 229 
 HIS   0.006   0.001   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (10189)
  covalent geometry    : angle       0.58718 (14374)
  hydrogen bonds       : bond        0.04098 (  327)
  hydrogen bonds       : angle       5.93276 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  289 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 289
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.9598 (mm-30) cc_final: 0.9397 (mm-30)
REVERT: A  112 LEU cc_start: 0.8858 (mp) cc_final: 0.8377 (tp)
REVERT: A  146 GLU cc_start: 0.9589 (tp30) cc_final: 0.9217 (tp30)
REVERT: A  266 ARG cc_start: 0.9638 (tpp-160) cc_final: 0.9310 (ttm-80)
REVERT: B    4 MET cc_start: 0.9424 (mmm) cc_final: 0.9133 (tpp)
REVERT: B   18 LEU cc_start: 0.9638 (tp) cc_final: 0.9333 (tp)
REVERT: B   22 GLU cc_start: 0.9585 (pt0) cc_final: 0.9322 (pt0)
REVERT: B   26 PHE cc_start: 0.9374 (m-80) cc_final: 0.8847 (m-80)
REVERT: B  171 HIS cc_start: 0.9390 (m-70) cc_final: 0.9027 (m-70)
REVERT: D   39 ASP cc_start: 0.9495 (m-30) cc_final: 0.9071 (p0)
REVERT: D  162 MET cc_start: 0.9160 (pmm) cc_final: 0.8944 (pmm)
REVERT: D  178 ASP cc_start: 0.7707 (m-30) cc_final: 0.7368 (m-30)
REVERT: D  220 TYR cc_start: 0.9240 (t80) cc_final: 0.8808 (t80)
REVERT: D  242 THR cc_start: 0.7540 (p) cc_final: 0.7003 (p)
REVERT: C   71 MET cc_start: 0.9213 (mmp) cc_final: 0.8975 (mmm)
REVERT: C  165 GLU cc_start: 0.8748 (mp0) cc_final: 0.8276 (mp0)
REVERT: C  265 PHE cc_start: 0.9731 (m-80) cc_final: 0.9436 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 289
  average time/residue: 0.1870
  time to fit residues: 73.0939
Evaluate side-chains
  258 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 111 optimal weight:    7.9990
   chunk 100 optimal weight:    0.0030
   chunk 2 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   chunk 3 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9990
   overall best weight:    1.9396

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

Flipped N/Q/H residues before XYZ refinement:
C  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.079385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.057946 restraints weight = 137712.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.060488 restraints weight = 78249.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.062346 restraints weight = 52952.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.063583 restraints weight = 40092.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.064491 restraints weight = 33185.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.8465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10189  Z= 0.152
  Angle     :  0.578   6.757  14374  Z= 0.303
  Chirality :  0.038   0.188   1788
  Planarity :  0.005   0.056   1512
  Dihedral  : 26.721 178.457   2716
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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 aren not related in a simple way.
  whole: -0.78 (0.27), residues: 1055
  helix:  0.31 (0.24), residues: 469
  sheet: -1.76 (0.36), residues: 195
  loop : -0.63 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 151 
 TYR   0.014   0.001   TYR B 225 
 PHE   0.014   0.001   PHE C 218 
 TRP   0.011   0.001   TRP B 229 
 HIS   0.006   0.001   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10189)
  covalent geometry    : angle       0.57827 (14374)
  hydrogen bonds       : bond        0.03961 (  327)
  hydrogen bonds       : angle       5.76762 (  934)

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

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

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2110 Ramachandran restraints generated.
    1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET    1 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LEU   18 is missing expected H atoms. Skipping.
Residue LEU   21 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue THR   91 is missing expected H atoms. Skipping.
Residue ILE   93 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue ILE  116 is missing expected H atoms. Skipping.
Residue LEU  122 is missing expected H atoms. Skipping.
Residue LEU  123 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue THR  136 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  194 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue LEU  279 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue VAL   34 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   37 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   82 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LEU  144 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue VAL  163 is missing expected H atoms. Skipping.
Residue THR  222 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue TYR  264 is missing expected H atoms. Skipping.
Residue MET    1 is missing expected H atoms. Skipping.
Residue LEU    3 is missing expected H atoms. Skipping.
Residue TYR   27 is missing expected H atoms. Skipping.
Residue VAL   29 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   40 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue ILE   49 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue ILE   66 is missing expected H atoms. Skipping.
Residue LEU   74 is missing expected H atoms. Skipping.
Residue LEU   85 is missing expected H atoms. Skipping.
Residue TYR   96 is missing expected H atoms. Skipping.
Residue LYS  108 is missing expected H atoms. Skipping.
Residue LYS  118 is missing expected H atoms. Skipping.
Residue LEU  126 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue LEU  153 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue VAL  183 is missing expected H atoms. Skipping.
Residue LEU  186 is missing expected H atoms. Skipping.
Residue LEU  195 is missing expected H atoms. Skipping.
Residue THR  199 is missing expected H atoms. Skipping.
Residue LEU  201 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue VAL  215 is missing expected H atoms. Skipping.
Residue LEU  228 is missing expected H atoms. Skipping.
Residue LEU  230 is missing expected H atoms. Skipping.
Residue MET  232 is missing expected H atoms. Skipping.
Residue THR  235 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue VAL  255 is missing expected H atoms. Skipping.
Residue TYR  256 is missing expected H atoms. Skipping.
Residue THR  278 is missing expected H atoms. Skipping.
Residue MET    4 is missing expected H atoms. Skipping.
Residue LYS   14 is missing expected H atoms. Skipping.
Residue MET   24 is missing expected H atoms. Skipping.
Residue LEU   32 is missing expected H atoms. Skipping.
Residue LEU   36 is missing expected H atoms. Skipping.
Residue LEU   44 is missing expected H atoms. Skipping.
Residue MET   60 is missing expected H atoms. Skipping.
Residue LEU   83 is missing expected H atoms. Skipping.
Residue ILE  133 is missing expected H atoms. Skipping.
Residue MET  139 is missing expected H atoms. Skipping.
Residue MET  147 is missing expected H atoms. Skipping.
Residue LYS  155 is missing expected H atoms. Skipping.
Residue LEU  160 is missing expected H atoms. Skipping.
Residue MET  162 is missing expected H atoms. Skipping.
Residue LYS  170 is missing expected H atoms. Skipping.
Residue ILE  173 is missing expected H atoms. Skipping.
Residue MET  198 is missing expected H atoms. Skipping.
Residue LYS  203 is missing expected H atoms. Skipping.
Residue LEU  241 is missing expected H atoms. Skipping.
Residue THR  242 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue SER  254 is missing expected H atoms. Skipping.
Residue ILE  257 is missing expected H atoms. Skipping.
Residue LEU  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Evaluate side-chains
  291 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 291
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9387 (mm-30)
REVERT: A   44 LEU cc_start: 0.9667 (mm) cc_final: 0.9463 (tp)
REVERT: A  146 GLU cc_start: 0.9578 (tp30) cc_final: 0.9213 (tp30)
REVERT: A  266 ARG cc_start: 0.9634 (tpp-160) cc_final: 0.9315 (ttm-80)
REVERT: B    4 MET cc_start: 0.9412 (mmm) cc_final: 0.9118 (tpp)
REVERT: B   18 LEU cc_start: 0.9641 (tp) cc_final: 0.9350 (tp)
REVERT: B   22 GLU cc_start: 0.9582 (pt0) cc_final: 0.9309 (pt0)
REVERT: B   26 PHE cc_start: 0.9381 (m-80) cc_final: 0.8838 (m-80)
REVERT: B  112 LEU cc_start: 0.9529 (tp) cc_final: 0.9313 (tp)
REVERT: B  119 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9353 (mt-10)
REVERT: B  171 HIS cc_start: 0.9379 (m-70) cc_final: 0.8984 (m-70)
REVERT: B  186 LEU cc_start: 0.9297 (mt) cc_final: 0.9049 (mt)
REVERT: D   39 ASP cc_start: 0.9489 (m-30) cc_final: 0.9079 (p0)
REVERT: D  220 TYR cc_start: 0.9233 (t80) cc_final: 0.8819 (t80)
REVERT: C   71 MET cc_start: 0.9213 (mmp) cc_final: 0.8966 (mmm)
REVERT: C  165 GLU cc_start: 0.8717 (mp0) cc_final: 0.8195 (mp0)
REVERT: C  265 PHE cc_start: 0.9710 (m-80) cc_final: 0.9409 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 291
  average time/residue: 0.1930
  time to fit residues: 75.8686
Evaluate side-chains
  262 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 13 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0470
   chunk 16 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.081694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.059401 restraints weight = 123829.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.062108 restraints weight = 69507.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.064089 restraints weight = 46622.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.065509 restraints weight = 35056.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.066475 restraints weight = 28520.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.8574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10189  Z= 0.101
  Angle     :  0.547   6.778  14374  Z= 0.282
  Chirality :  0.037   0.153   1788
  Planarity :  0.004   0.060   1512
  Dihedral  : 26.416 179.717   2716
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.27), residues: 1055
  helix:  0.88 (0.24), residues: 471
  sheet: -1.43 (0.37), residues: 193
  loop : -0.40 (0.35), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 151 
 TYR   0.012   0.001   TYR A 220 
 PHE   0.007   0.001   PHE C 218 
 TRP   0.008   0.001   TRP B 229 
 HIS   0.004   0.001   HIS D 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 (10189)
  covalent geometry    : angle       0.54733 (14374)
  hydrogen bonds       : bond        0.03528 (  327)
  hydrogen bonds       : angle       5.39714 (  934)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3390.99 seconds
wall clock time: 58 minutes 17.27 seconds (3497.27 seconds total)