Starting phenix.real_space_refine
on Sat Aug 23 01:03:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j20_35940/08_2025/8j20_35940.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j20_35940/08_2025/8j20_35940.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j20_35940/08_2025/8j20_35940.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j20_35940/08_2025/8j20_35940.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j20_35940/08_2025/8j20_35940.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j20_35940/08_2025/8j20_35940.cif"
  }
  resolution = 3.2
  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=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     Cl      2      4.86       5
     C    5634      2.51       5
     N    1497      2.21       5
     O    1641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  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: 8832
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2610
          Classifications: {'peptide': 340}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "B"
      Number of atoms: 1775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1775
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1791
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2188
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 13, 'TRANS': 260}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 433
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 35
          Unusual residues: {'9T4': 1, 'LEA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.09, per 1000 atoms: 0.24
  Number of scatterers: 8832
  At special positions: 0
  Unit cell: (111.28, 110.24, 122.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      58     16.00
     O    1641      8.00
     N    1497      7.00
     C    5634      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 197 " - pdb=" SG  CYS B 267 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  88 " - pdb=" SG  CYS D 169 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 290.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2092

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      37.6% alpha, 19.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 36
      removed outlier: 3.595A  pdb=" N   CYS A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 46
      removed outlier: 3.504A  pdb=" N   ILE A  44 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 94
      removed outlier: 3.936A  pdb=" N   GLY B  94 " --> pdb=" O   SER B  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 91 through 94'
    Processing helix  chain 'B' and resid 100 through 103
      removed outlier: 3.551A  pdb=" N   LYS B 103 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 100 through 103'
    Processing helix  chain 'B' and resid 125 through 129
      removed outlier: 4.015A  pdb=" N   THR B 129 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 6
      removed outlier: 3.766A  pdb=" N   SER C   6 " --> pdb=" O   CYS C   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 3 through 6'
    Processing helix  chain 'C' and resid 7 through 32
      removed outlier: 3.661A  pdb=" N   ALA C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG C  32 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 54
    Processing helix  chain 'C' and resid 207 through 212
      removed outlier: 4.372A  pdb=" N   TRP C 211 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 255
      removed outlier: 3.728A  pdb=" N   LYS C 248 " --> pdb=" O   HIS C 244 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LEU C 249 " --> pdb=" O   GLU C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 281
      removed outlier: 3.596A  pdb=" N   GLU C 275 " --> pdb=" O   LYS C 271 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLU C 276 " --> pdb=" O   ASP C 272 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   LYS C 280 " --> pdb=" O   GLU C 276 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER C 281 " --> pdb=" O   LYS C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 310
      removed outlier: 4.029A  pdb=" N   ALA C 301 " --> pdb=" O   GLU C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 351
    Processing helix  chain 'D' and resid 14 through 46
      removed outlier: 3.707A  pdb=" N   VAL D  20 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
      Proline residue:  D  30  - end of helix
      removed outlier: 3.958A  pdb=" N   VAL D  37 " --> pdb=" O   LEU D  33 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ILE D  38 " --> pdb=" O   LEU D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 73
      removed outlier: 3.623A  pdb=" N   ASP D  61 " --> pdb=" O   LEU D  57 " (cutoff:3.500A)
      Proline residue:  D  69  - end of helix
    Processing helix  chain 'D' and resid 87 through 119
      removed outlier: 3.522A  pdb=" N   TYR D 100 " --> pdb=" O   PHE D  96 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR D 102 " --> pdb=" O   THR D  98 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ALA D 103 " --> pdb=" O   ILE D  99 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU D 104 " --> pdb=" O   TYR D 100 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL D 117 " --> pdb=" O   ARG D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 126
    Processing helix  chain 'D' and resid 128 through 155
      removed outlier: 3.736A  pdb=" N   VAL D 150 " --> pdb=" O   HIS D 146 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   ILE D 153 " --> pdb=" O   VAL D 149 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU D 154 " --> pdb=" O   VAL D 150 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE D 155 " --> pdb=" O   TYR D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 211
      Proline residue:  D 183  - end of helix
      removed outlier: 3.880A  pdb=" N   VAL D 195 " --> pdb=" O   VAL D 191 " (cutoff:3.500A)
      Proline residue:  D 196  - end of helix
    Processing helix  chain 'D' and resid 216 through 252
      removed outlier: 4.438A  pdb=" N   ARG D 220 " --> pdb=" O   SER D 216 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   LEU D 226 " --> pdb=" O   ARG D 222 " (cutoff:3.500A)
      Proline residue:  D 240  - end of helix
      removed outlier: 3.766A  pdb=" N   TYR D 249 " --> pdb=" O   HIS D 245 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ILE D 250 " --> pdb=" O   VAL D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 257 through 280
      removed outlier: 4.044A  pdb=" N   VAL D 261 " --> pdb=" O   TRP D 257 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   LEU D 262 " --> pdb=" O   ARG D 258 " (cutoff:3.500A)
      Proline residue:  D 273  - end of helix
      removed outlier: 3.584A  pdb=" N   PHE D 278 " --> pdb=" O   LEU D 274 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   SER D 280 " --> pdb=" O   TYR D 276 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 280 through 291
      removed outlier: 3.826A  pdb=" N   GLU D 289 " --> pdb=" O   ALA D 285 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   LEU D 291 " --> pdb=" O   PHE D 287 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 7 through 24
      removed outlier: 3.654A  pdb=" N   GLN E  11 " --> pdb=" O   ALA E   7 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASN E  24 " --> pdb=" O   LYS E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84
      removed outlier: 6.064A  pdb=" N   LEU A  90 " --> pdb=" O   ALA A 103 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA A 103 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ILE A  92 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 126
      removed outlier: 6.407A  pdb=" N   CYS A 132 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   GLU A 149 " --> pdb=" O   CYS A 132 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ILE A 134 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ARG A 145 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 171
      removed outlier: 3.524A  pdb=" N   THR A 189 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   ASP A 181 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   GLN A 187 " --> pdb=" O   ASP A 181 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199
      removed outlier: 3.651A  pdb=" N   PHE A 210 " --> pdb=" O   TRP A 222 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN A 231 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ASP A 223 " --> pdb=" O   CYS A 229 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   CYS A 229 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243
      removed outlier: 3.739A  pdb=" N   SER A 256 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   THR A 260 " --> pdb=" O   SER A 256 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   CYS A 261 " --> pdb=" O   THR A 274 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   THR A 274 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   LEU A 263 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLN A 270 " --> pdb=" O   ASP A 265 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 289
      removed outlier: 4.665A  pdb=" N   VAL A 287 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   LEU A 297 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   PHE A 289 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   LEU A 295 " --> pdb=" O   PHE A 289 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   CYS A 305 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   VAL A 318 " --> pdb=" O   CYS A 305 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL A 307 " --> pdb=" O   ALA A 316 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45
      removed outlier: 3.587A  pdb=" N   THR B 116 " --> pdb=" O   ASP B 111 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50
      removed outlier: 6.151A  pdb=" N   GLY B  48 " --> pdb=" O   THR B 156 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   MET B  72 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   TYR B  88 " --> pdb=" O   MET B  72 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP B  74 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 50
      removed outlier: 6.151A  pdb=" N   GLY B  48 " --> pdb=" O   THR B 156 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   PHE B 148 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 179
    Processing sheet with id=AB3, first strand: chain 'B' and resid 184 through 185
      removed outlier: 3.541A  pdb=" N   GLY B 263 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LEU B 212 " --> pdb=" O   TYR B 228 " (cutoff:3.500A)
      removed outlier: 4.631A  pdb=" N   TYR B 228 " --> pdb=" O   LEU B 212 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   TRP B 214 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 196 through 200
      removed outlier: 6.490A  pdb=" N   LYS C  35 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 7.521A  pdb=" N   ILE C 222 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   LEU C  37 " --> pdb=" O   ILE C 222 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   CYS C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU C  39 " --> pdb=" O   CYS C 224 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   ALA C 226 " --> pdb=" O   LEU C  39 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1425
        1.31 -     1.44: 2509
        1.44 -     1.56: 5002
        1.56 -     1.69: 2
        1.69 -     1.82: 84
  Bond restraints: 9022
  Sorted by residual:
  bond pdb=" C13 9T4 D 401 "
       pdb=" C16 9T4 D 401 "
    ideal  model  delta    sigma   weight residual
    1.342  1.523 -0.181 2.00e-02 2.50e+03 8.20e+01
  bond pdb=" C09 9T4 D 401 "
       pdb=" C10 9T4 D 401 "
    ideal  model  delta    sigma   weight residual
    1.359  1.523 -0.164 2.00e-02 2.50e+03 6.70e+01
  bond pdb=" C27 9T4 D 401 "
       pdb=" C28 9T4 D 401 "
    ideal  model  delta    sigma   weight residual
    1.384  1.529 -0.145 2.00e-02 2.50e+03 5.24e+01
  bond pdb=" C26 9T4 D 401 "
       pdb=" C28 9T4 D 401 "
    ideal  model  delta    sigma   weight residual
    1.386  1.529 -0.143 2.00e-02 2.50e+03 5.13e+01
  bond pdb=" C24 9T4 D 401 "
       pdb=" C27 9T4 D 401 "
    ideal  model  delta    sigma   weight residual
    1.385  1.528 -0.143 2.00e-02 2.50e+03 5.08e+01
  ... (remaining 9017 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.99: 12180
        3.99 -     7.99: 37
        7.99 -    11.98: 3
       11.98 -    15.98: 3
       15.98 -    19.97: 3
  Bond angle restraints: 12226
  Sorted by residual:
  angle pdb=" C   TYR B 273 "
        pdb=" N   PRO B 274 "
        pdb=" CA  PRO B 274 "
      ideal   model   delta    sigma   weight residual
     119.84  132.52  -12.68 1.25e+00 6.40e-01 1.03e+02
  angle pdb=" N   TYR B 273 "
        pdb=" CA  TYR B 273 "
        pdb=" C   TYR B 273 "
      ideal   model   delta    sigma   weight residual
     109.81  129.78  -19.97 2.21e+00 2.05e-01 8.17e+01
  angle pdb=" C   PRO B 274 "
        pdb=" CA  PRO B 274 "
        pdb=" CB  PRO B 274 "
      ideal   model   delta    sigma   weight residual
     111.56  124.57  -13.01 1.65e+00 3.67e-01 6.22e+01
  angle pdb=" C   GLU B 272 "
        pdb=" N   TYR B 273 "
        pdb=" CA  TYR B 273 "
      ideal   model   delta    sigma   weight residual
     121.80  135.07  -13.27 2.44e+00 1.68e-01 2.96e+01
  angle pdb=" CA  PRO B 274 "
        pdb=" N   PRO B 274 "
        pdb=" CD  PRO B 274 "
      ideal   model   delta    sigma   weight residual
     112.00  104.86    7.14 1.40e+00 5.10e-01 2.60e+01
  ... (remaining 12221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.59: 4776
       23.59 -    47.18: 502
       47.18 -    70.77: 65
       70.77 -    94.37: 9
       94.37 -   117.96: 1
  Dihedral angle restraints: 5353
    sinusoidal: 2103
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  TYR B 273 "
           pdb=" C   TYR B 273 "
           pdb=" N   PRO B 274 "
           pdb=" CA  PRO B 274 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00   62.04  117.96     0      5.00e+00 4.00e-02 5.57e+02
  dihedral pdb=" C   TYR B 273 "
           pdb=" N   TYR B 273 "
           pdb=" CA  TYR B 273 "
           pdb=" CB  TYR B 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -150.58   27.98     0      2.50e+00 1.60e-01 1.25e+02
  dihedral pdb=" N   TYR B 273 "
           pdb=" C   TYR B 273 "
           pdb=" CA  TYR B 273 "
           pdb=" CB  TYR B 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  150.30  -27.50     0      2.50e+00 1.60e-01 1.21e+02
  ... (remaining 5350 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.257: 1380
       0.257 -    0.514: 0
       0.514 -    0.771: 1
       0.771 -    1.028: 0
       1.028 -    1.286: 1
  Chirality restraints: 1382
  Sorted by residual:
  chirality pdb=" CA  TYR B 273 "
            pdb=" N   TYR B 273 "
            pdb=" C   TYR B 273 "
            pdb=" CB  TYR B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.22    1.29 2.00e-01 2.50e+01 4.13e+01
  chirality pdb=" CA  PRO B 274 "
            pdb=" N   PRO B 274 "
            pdb=" C   PRO B 274 "
            pdb=" CB  PRO B 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.07    0.64 2.00e-01 2.50e+01 1.04e+01
  chirality pdb=" C08 9T4 D 401 "
            pdb=" C09 9T4 D 401 "
            pdb=" C13 9T4 D 401 "
            pdb=" C17 9T4 D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 1379 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 273 "   -0.066 5.00e-02 4.00e+02   9.65e-02 1.49e+01
        pdb=" N   PRO B 274 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO B 274 "   -0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO B 274 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 272 "    0.058 5.00e-02 4.00e+02   8.75e-02 1.23e+01
        pdb=" N   PRO D 273 "   -0.151 5.00e-02 4.00e+02
        pdb=" CA  PRO D 273 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO D 273 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D 239 "   -0.031 5.00e-02 4.00e+02   4.68e-02 3.50e+00
        pdb=" N   PRO D 240 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO D 240 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 240 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 675
        2.74 -     3.28: 8615
        3.28 -     3.82: 14912
        3.82 -     4.36: 17012
        4.36 -     4.90: 29893
  Nonbonded interactions: 71107
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 211 "
            pdb=" OG  SER C   6 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER A 342 "
            pdb=" OD1 ASP A 344 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER A 172 "
            pdb=" OD1 ASP A 174 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   SER A  78 "
            pdb=" OG  SER A  78 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   LEU D 197 "
            pdb=" OG  SER D 201 "
     model   vdw
     2.269 3.040
  ... (remaining 71102 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.01 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.080
  Find NCS groups from input model:        0.040
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
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      :  0.006   0.181   9025  Z= 0.281
  Angle     :  0.709  19.972  12232  Z= 0.355
  Chirality :  0.057   1.286   1382
  Planarity :  0.005   0.097   1544
  Dihedral  : 17.895 117.958   3252
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  :  4.43 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 35.69 %
    Favored  : 63.68 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.09 %

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:  0.12 (0.26), residues: 1107
  helix:  1.66 (0.28), residues: 355
  sheet:  0.71 (0.33), residues: 243
  loop : -1.45 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  71 
 TYR   0.011   0.001   TYR D 202 
 PHE   0.017   0.001   PHE A 210 
 TRP   0.018   0.001   TRP D  15 
 HIS   0.006   0.001   HIS B 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 9022)
  covalent geometry    : angle       0.70900 (12226)
  SS BOND              : bond        0.00320 (    3)
  SS BOND              : angle       1.05933 (    6)
  hydrogen bonds       : bond        0.15627 (  396)
  hydrogen bonds       : angle       6.26383 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 197
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7726 (mm110)
REVERT: A  163 LEU cc_start: 0.7931 (mm) cc_final: 0.7715 (mt)
  outliers start: 6
  outliers final: 3
  residues processed: 199
  average time/residue: 0.0907
  time to fit residues: 24.0040
Evaluate side-chains
  195 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 192
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  220 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0270
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0040
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    9.9990
   overall best weight:    0.4850

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

Flipped N/Q/H residues before XYZ refinement:
B 180 GLN
B 217 GLN
C 195 HIS
** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.160875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.140089 restraints weight = 13113.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.29
r_work: 0.3601 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3431 r_free = 0.3431    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
r_final: 0.3431
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   9025  Z= 0.148
  Angle     :  0.636  13.818  12232  Z= 0.320
  Chirality :  0.044   0.376   1382
  Planarity :  0.004   0.064   1544
  Dihedral  :  6.001  58.131   1268
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.79 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 30.70 %
    Favored  : 64.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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:  0.12 (0.26), residues: 1107
  helix:  1.48 (0.27), residues: 381
  sheet:  0.86 (0.34), residues: 236
  loop : -1.52 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  71 
 TYR   0.014   0.001   TYR B 228 
 PHE   0.022   0.001   PHE D  95 
 TRP   0.011   0.001   TRP D  15 
 HIS   0.004   0.001   HIS D  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 9022)
  covalent geometry    : angle       0.63614 (12226)
  SS BOND              : bond        0.00187 (    3)
  SS BOND              : angle       0.92438 (    6)
  hydrogen bonds       : bond        0.04091 (  396)
  hydrogen bonds       : angle       4.95882 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 223
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6221 (p0)
REVERT: A   72 MET cc_start: 0.6974 (mmt) cc_final: 0.6678 (mmt)
REVERT: A  111 VAL cc_start: 0.7552 (m) cc_final: 0.7313 (p)
REVERT: A  140 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7258 (mmp80)
REVERT: A  163 LEU cc_start: 0.8041 (mm) cc_final: 0.7706 (mp)
REVERT: A  269 ASP cc_start: 0.7777 (t0) cc_final: 0.7544 (t0)
REVERT: A  297 LEU cc_start: 0.8229 (mp) cc_final: 0.8021 (mp)
REVERT: B  177 VAL cc_start: 0.8092 (m) cc_final: 0.7870 (p)
REVERT: B  237 VAL cc_start: 0.8065 (t) cc_final: 0.7841 (p)
REVERT: B  271 LEU cc_start: 0.7839 (mt) cc_final: 0.7608 (mt)
REVERT: C  189 PHE cc_start: 0.7016 (p90) cc_final: 0.6753 (p90)
REVERT: C  200 ASP cc_start: 0.7966 (t0) cc_final: 0.7702 (t0)
REVERT: C  283 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7815 (mp)
REVERT: C  306 GLN cc_start: 0.6244 (mm110) cc_final: 0.5964 (mm110)
REVERT: C  316 THR cc_start: 0.7451 (p) cc_final: 0.7187 (t)
REVERT: D   29 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7298 (mt)
  outliers start: 46
  outliers final: 25
  residues processed: 248
  average time/residue: 0.0939
  time to fit residues: 31.2394
Evaluate side-chains
  244 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 216
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ASP
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   20 ASP
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  283 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   87 LEU
Chi-restraints excluded: chain D residue  110 SER
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  226 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 109 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 25 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9990
   chunk 96 optimal weight:    0.0570
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
A 231 GLN
C 241 ASN
D 284 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.153380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132293 restraints weight = 13134.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.25
r_work: 0.3560 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3408 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       36 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9025  Z= 0.134
  Angle     :  0.600  12.460  12232  Z= 0.304
  Chirality :  0.044   0.275   1382
  Planarity :  0.004   0.052   1544
  Dihedral  :  5.713  56.026   1264
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.79 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 31.63 %
    Favored  : 63.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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:  0.05 (0.25), residues: 1107
  helix:  1.50 (0.27), residues: 381
  sheet:  0.53 (0.33), residues: 249
  loop : -1.51 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 220 
 TYR   0.014   0.001   TYR B 141 
 PHE   0.016   0.001   PHE D  95 
 TRP   0.010   0.001   TRP D  15 
 HIS   0.003   0.001   HIS A 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9022)
  covalent geometry    : angle       0.59996 (12226)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       0.78361 (    6)
  hydrogen bonds       : bond        0.03686 (  396)
  hydrogen bonds       : angle       4.76691 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 215
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.6943 (mmt) cc_final: 0.6530 (mmt)
REVERT: A  111 VAL cc_start: 0.7597 (m) cc_final: 0.7379 (p)
REVERT: A  112 MET cc_start: 0.7895 (ptp) cc_final: 0.7452 (ptp)
REVERT: A  135 TYR cc_start: 0.8961 (m-80) cc_final: 0.8322 (m-80)
REVERT: A  222 TRP cc_start: 0.8324 (m100) cc_final: 0.8002 (m100)
REVERT: A  269 ASP cc_start: 0.7721 (t0) cc_final: 0.7445 (t0)
REVERT: A  326 VAL cc_start: 0.8009 (t) cc_final: 0.7624 (p)
REVERT: B  177 VAL cc_start: 0.8124 (m) cc_final: 0.7903 (p)
REVERT: B  179 THR cc_start: 0.8299 (p) cc_final: 0.8059 (t)
REVERT: B  237 VAL cc_start: 0.8049 (t) cc_final: 0.7817 (p)
REVERT: C   14 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7319 (mt-10)
REVERT: C   17 LYS cc_start: 0.8291 (mttm) cc_final: 0.8038 (mmtm)
REVERT: C   33 GLU cc_start: 0.7084 (tt0) cc_final: 0.6722 (tt0)
REVERT: C  197 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7483 (mttm)
REVERT: C  200 ASP cc_start: 0.8064 (t0) cc_final: 0.7734 (t0)
REVERT: C  306 GLN cc_start: 0.6351 (mm110) cc_final: 0.5965 (mm110)
REVERT: C  316 THR cc_start: 0.7492 (p) cc_final: 0.7197 (t)
REVERT: D   18 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6887 (p90)
REVERT: D   29 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7076 (mt)
REVERT: D   66 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6379 (pp)
  outliers start: 50
  outliers final: 25
  residues processed: 245
  average time/residue: 0.0834
  time to fit residues: 27.9759
Evaluate side-chains
  240 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 211
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  197 LYS
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   66 LEU
Chi-restraints excluded: chain D residue  110 SER
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  290 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 42 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.153530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.132333 restraints weight = 13021.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.22
r_work: 0.3510 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9025  Z= 0.164
  Angle     :  0.637  14.176  12232  Z= 0.319
  Chirality :  0.045   0.300   1382
  Planarity :  0.005   0.088   1544
  Dihedral  :  5.560  52.675   1262
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.42 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 30.70 %
    Favored  : 63.89 %
  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: -0.15 (0.26), residues: 1107
  helix:  1.28 (0.27), residues: 390
  sheet:  0.16 (0.32), residues: 261
  loop : -1.49 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  71 
 TYR   0.015   0.002   TYR B 141 
 PHE   0.018   0.002   PHE A 210 
 TRP   0.011   0.001   TRP A 180 
 HIS   0.004   0.001   HIS C 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9022)
  covalent geometry    : angle       0.63712 (12226)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       1.04202 (    6)
  hydrogen bonds       : bond        0.03614 (  396)
  hydrogen bonds       : angle       4.84969 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 217
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.8046 (ptp-170) cc_final: 0.7818 (ptp-170)
REVERT: A   72 MET cc_start: 0.7145 (mmt) cc_final: 0.6760 (mmt)
REVERT: A  111 VAL cc_start: 0.7659 (m) cc_final: 0.7456 (p)
REVERT: A  112 MET cc_start: 0.7959 (ptp) cc_final: 0.7557 (ptp)
REVERT: A  129 ASP cc_start: 0.7693 (p0) cc_final: 0.7342 (p0)
REVERT: A  130 ASN cc_start: 0.7435 (m-40) cc_final: 0.7179 (m110)
REVERT: A  135 TYR cc_start: 0.8981 (m-80) cc_final: 0.8517 (m-80)
REVERT: A  163 LEU cc_start: 0.8134 (mm) cc_final: 0.7928 (mt)
REVERT: A  269 ASP cc_start: 0.7778 (t0) cc_final: 0.7453 (t0)
REVERT: B  177 VAL cc_start: 0.8186 (m) cc_final: 0.7960 (p)
REVERT: B  179 THR cc_start: 0.8284 (p) cc_final: 0.8031 (t)
REVERT: B  237 VAL cc_start: 0.8049 (t) cc_final: 0.7825 (p)
REVERT: C   17 LYS cc_start: 0.8320 (mttm) cc_final: 0.8067 (mmtm)
REVERT: C  200 ASP cc_start: 0.8099 (t0) cc_final: 0.7758 (t0)
REVERT: C  245 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6964 (tm-30)
REVERT: C  306 GLN cc_start: 0.6445 (mm110) cc_final: 0.6045 (mm110)
REVERT: C  316 THR cc_start: 0.7547 (p) cc_final: 0.7262 (t)
REVERT: D   18 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6935 (p90)
REVERT: D   29 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7277 (mt)
REVERT: D   71 ARG cc_start: 0.6831 (ttp80) cc_final: 0.6279 (ttp-110)
  outliers start: 52
  outliers final: 37
  residues processed: 247
  average time/residue: 0.0902
  time to fit residues: 30.0063
Evaluate side-chains
  248 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 209
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain C residue  341 ASP
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   29 LEU
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue  110 SER
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  290 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0170
   chunk 66 optimal weight:    0.3980
   chunk 98 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.154221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.132271 restraints weight = 13110.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.31
r_work: 0.3485 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3322
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3322 r_free = 0.3322    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       49 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9025  Z= 0.146
  Angle     :  0.618  14.582  12232  Z= 0.309
  Chirality :  0.043   0.251   1382
  Planarity :  0.005   0.084   1544
  Dihedral  :  5.599  53.464   1262
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.79 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 31.01 %
    Favored  : 64.00 %
  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: -0.24 (0.25), residues: 1107
  helix:  1.23 (0.27), residues: 392
  sheet:  0.03 (0.32), residues: 262
  loop : -1.52 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 220 
 TYR   0.014   0.001   TYR B 141 
 PHE   0.014   0.001   PHE A 210 
 TRP   0.010   0.001   TRP A 180 
 HIS   0.003   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9022)
  covalent geometry    : angle       0.61771 (12226)
  SS BOND              : bond        0.00388 (    3)
  SS BOND              : angle       0.89324 (    6)
  hydrogen bonds       : bond        0.03415 (  396)
  hydrogen bonds       : angle       4.79468 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 216
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   57 ARG cc_start: 0.8311 (ptp-170) cc_final: 0.8066 (ptp-170)
REVERT: A   60 ARG cc_start: 0.7371 (mmp80) cc_final: 0.7141 (mmp80)
REVERT: A   72 MET cc_start: 0.7162 (mmt) cc_final: 0.6721 (mmt)
REVERT: A  111 VAL cc_start: 0.7728 (m) cc_final: 0.7480 (p)
REVERT: A  112 MET cc_start: 0.7925 (ptp) cc_final: 0.7558 (ptp)
REVERT: A  135 TYR cc_start: 0.8989 (m-80) cc_final: 0.8626 (m-80)
REVERT: A  269 ASP cc_start: 0.7836 (t0) cc_final: 0.7519 (t0)
REVERT: B  179 THR cc_start: 0.8262 (p) cc_final: 0.8037 (t)
REVERT: C   17 LYS cc_start: 0.8314 (mttm) cc_final: 0.8077 (mmtm)
REVERT: C   33 GLU cc_start: 0.7398 (tt0) cc_final: 0.7108 (tt0)
REVERT: C  189 PHE cc_start: 0.7596 (p90) cc_final: 0.6947 (p90)
REVERT: C  197 LYS cc_start: 0.7982 (mttm) cc_final: 0.7499 (mttm)
REVERT: C  200 ASP cc_start: 0.8102 (t0) cc_final: 0.7799 (t0)
REVERT: C  245 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6960 (tm-30)
REVERT: C  306 GLN cc_start: 0.6453 (mm110) cc_final: 0.6049 (mm110)
REVERT: C  316 THR cc_start: 0.7492 (p) cc_final: 0.7197 (t)
REVERT: D   18 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6955 (p90)
REVERT: D   52 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7368 (m)
REVERT: D   68 LEU cc_start: 0.8689 (mt) cc_final: 0.8227 (tt)
  outliers start: 48
  outliers final: 37
  residues processed: 241
  average time/residue: 0.0967
  time to fit residues: 31.2549
Evaluate side-chains
  256 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 217
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain C residue  341 ASP
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  110 SER
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  290 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0030
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 108 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
A 166 ASN
E  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.150944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.128918 restraints weight = 12975.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.29
r_work: 0.3447 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3287
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3287 r_free = 0.3287    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
r_final: 0.3287
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9025  Z= 0.183
  Angle     :  0.657  14.632  12232  Z= 0.328
  Chirality :  0.045   0.256   1382
  Planarity :  0.005   0.080   1544
  Dihedral  :  5.745  51.805   1262
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.51 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 30.07 %
    Favored  : 63.79 %
  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: -0.36 (0.25), residues: 1107
  helix:  1.16 (0.27), residues: 394
  sheet: -0.12 (0.32), residues: 258
  loop : -1.57 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  71 
 TYR   0.016   0.002   TYR B 141 
 PHE   0.019   0.002   PHE A 210 
 TRP   0.012   0.001   TRP A 180 
 HIS   0.005   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 9022)
  covalent geometry    : angle       0.65643 (12226)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       0.90057 (    6)
  hydrogen bonds       : bond        0.03642 (  396)
  hydrogen bonds       : angle       4.92301 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 229
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.8327 (ptp-170) cc_final: 0.8037 (ptp-170)
REVERT: A   60 ARG cc_start: 0.7493 (mmp80) cc_final: 0.6972 (mmp80)
REVERT: A   72 MET cc_start: 0.7253 (mmt) cc_final: 0.6763 (mmt)
REVERT: A  114 CYS cc_start: 0.7338 (m) cc_final: 0.7107 (m)
REVERT: A  129 ASP cc_start: 0.7773 (p0) cc_final: 0.7440 (p0)
REVERT: A  135 TYR cc_start: 0.9013 (m-80) cc_final: 0.8682 (m-80)
REVERT: A  230 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7467 (mtm180)
REVERT: A  269 ASP cc_start: 0.7788 (t0) cc_final: 0.7403 (t0)
REVERT: B  179 THR cc_start: 0.8266 (p) cc_final: 0.8023 (t)
REVERT: C   17 LYS cc_start: 0.8310 (mttm) cc_final: 0.8062 (mmtm)
REVERT: C  189 PHE cc_start: 0.7683 (p90) cc_final: 0.6985 (p90)
REVERT: C  200 ASP cc_start: 0.8099 (t0) cc_final: 0.7804 (t0)
REVERT: C  245 GLU cc_start: 0.7304 (tm-30) cc_final: 0.7000 (tm-30)
REVERT: C  306 GLN cc_start: 0.6441 (mm110) cc_final: 0.6022 (mm110)
REVERT: D   18 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7091 (p90)
REVERT: D   52 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7380 (m)
REVERT: D   71 ARG cc_start: 0.6676 (ttp80) cc_final: 0.5847 (ttp-110)
REVERT: D  274 LEU cc_start: 0.7856 (tp) cc_final: 0.7247 (tp)
REVERT: D  278 PHE cc_start: 0.6847 (p90) cc_final: 0.6478 (p90)
  outliers start: 59
  outliers final: 46
  residues processed: 259
  average time/residue: 0.0870
  time to fit residues: 30.4422
Evaluate side-chains
  269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 221
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  257 ASP
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  121 MET
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain C residue  341 ASP
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain D residue  290 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 110 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0270
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
A 166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.151950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.129995 restraints weight = 13044.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.30
r_work: 0.3459 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3303 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       50 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9025  Z= 0.147
  Angle     :  0.636  14.832  12232  Z= 0.317
  Chirality :  0.043   0.244   1382
  Planarity :  0.005   0.077   1544
  Dihedral  :  5.771  54.422   1262
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  4.79 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 29.14 %
    Favored  : 64.31 %
  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: -0.39 (0.25), residues: 1107
  helix:  1.15 (0.27), residues: 394
  sheet: -0.36 (0.31), residues: 265
  loop : -1.45 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 220 
 TYR   0.015   0.001   TYR B 141 
 PHE   0.015   0.001   PHE A 210 
 TRP   0.011   0.001   TRP A 180 
 HIS   0.004   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9022)
  covalent geometry    : angle       0.63578 (12226)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       0.69899 (    6)
  hydrogen bonds       : bond        0.03411 (  396)
  hydrogen bonds       : angle       4.86639 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 222
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 ARG cc_start: 0.7447 (mmp80) cc_final: 0.6884 (mmp80)
REVERT: A   72 MET cc_start: 0.7209 (mmt) cc_final: 0.6728 (mmt)
REVERT: A  129 ASP cc_start: 0.7768 (p0) cc_final: 0.7378 (p0)
REVERT: A  135 TYR cc_start: 0.8983 (m-80) cc_final: 0.8674 (m-80)
REVERT: A  230 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7446 (mtm180)
REVERT: A  269 ASP cc_start: 0.7819 (t0) cc_final: 0.7450 (t0)
REVERT: B  155 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6714 (tt)
REVERT: B  179 THR cc_start: 0.8278 (p) cc_final: 0.8006 (t)
REVERT: C   17 LYS cc_start: 0.8284 (mttm) cc_final: 0.8038 (mmtm)
REVERT: C   33 GLU cc_start: 0.7389 (tt0) cc_final: 0.7119 (tt0)
REVERT: C  189 PHE cc_start: 0.7703 (p90) cc_final: 0.6946 (p90)
REVERT: C  197 LYS cc_start: 0.8040 (mttm) cc_final: 0.7515 (mttm)
REVERT: C  200 ASP cc_start: 0.8080 (t0) cc_final: 0.7787 (t0)
REVERT: C  245 GLU cc_start: 0.7321 (tm-30) cc_final: 0.7022 (tm-30)
REVERT: C  317 LYS cc_start: 0.7191 (mtmm) cc_final: 0.6761 (mtmt)
REVERT: D   18 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7101 (p90)
REVERT: D   52 VAL cc_start: 0.7799 (p) cc_final: 0.7421 (m)
REVERT: D   59 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7744 (pt)
REVERT: D   72 MET cc_start: 0.6888 (ttt) cc_final: 0.6629 (ttt)
REVERT: D  274 LEU cc_start: 0.7887 (tp) cc_final: 0.7301 (tp)
REVERT: D  278 PHE cc_start: 0.6869 (p90) cc_final: 0.6468 (p90)
  outliers start: 63
  outliers final: 47
  residues processed: 254
  average time/residue: 0.0863
  time to fit residues: 29.7713
Evaluate side-chains
  263 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 213
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  122 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  207 GLU
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain C residue  341 ASP
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  182 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain E residue   50 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0470
   chunk 63 optimal weight:    0.9980
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.153373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.132299 restraints weight = 12994.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 2.19
r_work: 0.3489 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3336 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3319
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3319 r_free = 0.3319    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       51 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9025  Z= 0.176
  Angle     :  0.668  14.980  12232  Z= 0.332
  Chirality :  0.045   0.250   1382
  Planarity :  0.005   0.076   1544
  Dihedral  :  5.861  53.565   1262
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  5.51 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 29.97 %
    Favored  : 63.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.45 (0.25), residues: 1107
  helix:  1.07 (0.26), residues: 394
  sheet: -0.19 (0.31), residues: 258
  loop : -1.58 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D 220 
 TYR   0.015   0.002   TYR B 141 
 PHE   0.025   0.002   PHE B 106 
 TRP   0.010   0.001   TRP A 180 
 HIS   0.005   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 9022)
  covalent geometry    : angle       0.66777 (12226)
  SS BOND              : bond        0.00342 (    3)
  SS BOND              : angle       0.99146 (    6)
  hydrogen bonds       : bond        0.03552 (  396)
  hydrogen bonds       : angle       4.91781 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 221
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.7079 (m)
REVERT: A   72 MET cc_start: 0.7216 (mmt) cc_final: 0.6680 (mmt)
REVERT: A  129 ASP cc_start: 0.7732 (p0) cc_final: 0.7384 (p0)
REVERT: A  135 TYR cc_start: 0.8937 (m-80) cc_final: 0.8590 (m-80)
REVERT: A  208 ARG cc_start: 0.8336 (tpt-90) cc_final: 0.8115 (tpt-90)
REVERT: A  230 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7461 (mtm180)
REVERT: A  238 SER cc_start: 0.8582 (m) cc_final: 0.8304 (t)
REVERT: A  257 ASP cc_start: 0.7427 (p0) cc_final: 0.7093 (p0)
REVERT: A  269 ASP cc_start: 0.7947 (t0) cc_final: 0.7562 (t0)
REVERT: B  155 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6694 (tt)
REVERT: B  179 THR cc_start: 0.8251 (p) cc_final: 0.7988 (t)
REVERT: B  268 MET cc_start: 0.8225 (ttp) cc_final: 0.7837 (ttm)
REVERT: C   17 LYS cc_start: 0.8382 (mttm) cc_final: 0.8145 (mmtm)
REVERT: C  200 ASP cc_start: 0.8081 (t0) cc_final: 0.7786 (t0)
REVERT: C  245 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: C  317 LYS cc_start: 0.7386 (mtmm) cc_final: 0.6996 (mtmt)
REVERT: D   18 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7110 (p90)
REVERT: D   52 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7418 (m)
REVERT: D   59 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7782 (pt)
  outliers start: 61
  outliers final: 48
  residues processed: 252
  average time/residue: 0.0927
  time to fit residues: 31.4823
Evaluate side-chains
  275 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 222
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  164 ASP
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  209 LYS
Chi-restraints excluded: chain C residue  216 GLU
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain C residue  341 ASP
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   52 VAL
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain E residue   50 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 98 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 19 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0050
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.154301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.133268 restraints weight = 13063.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.21
r_work: 0.3504 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       53 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9025  Z= 0.140
  Angle     :  0.635  14.949  12232  Z= 0.317
  Chirality :  0.044   0.311   1382
  Planarity :  0.005   0.066   1544
  Dihedral  :  5.947  55.786   1262
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.24 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 30.59 %
    Favored  : 63.48 %
  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: -0.39 (0.25), residues: 1107
  helix:  1.21 (0.27), residues: 388
  sheet: -0.36 (0.31), residues: 264
  loop : -1.47 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 220 
 TYR   0.015   0.001   TYR B 228 
 PHE   0.037   0.002   PHE D 278 
 TRP   0.009   0.001   TRP A 180 
 HIS   0.004   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9022)
  covalent geometry    : angle       0.63501 (12226)
  SS BOND              : bond        0.00290 (    3)
  SS BOND              : angle       0.77225 (    6)
  hydrogen bonds       : bond        0.03344 (  396)
  hydrogen bonds       : angle       4.87068 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 223
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.7209 (mmt) cc_final: 0.6677 (mmt)
REVERT: A  129 ASP cc_start: 0.7718 (p0) cc_final: 0.7386 (p0)
REVERT: A  135 TYR cc_start: 0.8912 (m-80) cc_final: 0.8531 (m-80)
REVERT: A  158 SER cc_start: 0.7829 (OUTLIER) cc_final: 0.7349 (p)
REVERT: A  208 ARG cc_start: 0.8236 (tpt-90) cc_final: 0.8010 (tpt-90)
REVERT: A  230 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7480 (mtm180)
REVERT: A  238 SER cc_start: 0.8593 (m) cc_final: 0.8316 (t)
REVERT: A  269 ASP cc_start: 0.7769 (t0) cc_final: 0.7287 (t0)
REVERT: B  155 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6743 (tt)
REVERT: B  179 THR cc_start: 0.8237 (p) cc_final: 0.7975 (t)
REVERT: C   17 LYS cc_start: 0.8381 (mttm) cc_final: 0.8168 (mmtm)
REVERT: C   33 GLU cc_start: 0.7365 (tt0) cc_final: 0.6989 (tt0)
REVERT: C  197 LYS cc_start: 0.7970 (mttm) cc_final: 0.7569 (mttm)
REVERT: C  200 ASP cc_start: 0.8061 (t0) cc_final: 0.7754 (t0)
REVERT: C  245 GLU cc_start: 0.7339 (tm-30) cc_final: 0.6922 (tm-30)
REVERT: C  317 LYS cc_start: 0.7281 (mtmm) cc_final: 0.6686 (mtmt)
REVERT: D   52 VAL cc_start: 0.7781 (p) cc_final: 0.7390 (m)
REVERT: D   59 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7796 (pt)
  outliers start: 57
  outliers final: 45
  residues processed: 251
  average time/residue: 0.1055
  time to fit residues: 35.2587
Evaluate side-chains
  260 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 212
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  207 GLU
Chi-restraints excluded: chain C residue  209 LYS
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain C residue  341 ASP
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain D residue  290 LEU
Chi-restraints excluded: chain E residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0030
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.152996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.132327 restraints weight = 13046.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.16
r_work: 0.3497 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3330
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3330 r_free = 0.3330    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9025  Z= 0.162
  Angle     :  0.665  15.003  12232  Z= 0.330
  Chirality :  0.046   0.314   1382
  Planarity :  0.005   0.072   1544
  Dihedral  :  6.046  56.436   1262
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.60 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 31.53 %
    Favored  : 63.16 %
  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: -0.43 (0.25), residues: 1107
  helix:  1.13 (0.26), residues: 391
  sheet: -0.20 (0.31), residues: 263
  loop : -1.59 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 220 
 TYR   0.016   0.002   TYR B 141 
 PHE   0.036   0.002   PHE D 278 
 TRP   0.010   0.001   TRP A 180 
 HIS   0.004   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9022)
  covalent geometry    : angle       0.66484 (12226)
  SS BOND              : bond        0.00394 (    3)
  SS BOND              : angle       0.79853 (    6)
  hydrogen bonds       : bond        0.03453 (  396)
  hydrogen bonds       : angle       4.96450 ( 1143)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 213
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ARG cc_start: 0.7518 (mmp80) cc_final: 0.7315 (mmp80)
REVERT: A   72 MET cc_start: 0.7244 (mmt) cc_final: 0.6754 (mmt)
REVERT: A  129 ASP cc_start: 0.7765 (p0) cc_final: 0.7436 (p0)
REVERT: A  135 TYR cc_start: 0.8900 (m-80) cc_final: 0.8577 (m-80)
REVERT: A  208 ARG cc_start: 0.8248 (tpt-90) cc_final: 0.8037 (tpt-90)
REVERT: A  230 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7511 (mtm180)
REVERT: A  238 SER cc_start: 0.8580 (m) cc_final: 0.8311 (t)
REVERT: A  269 ASP cc_start: 0.7803 (t0) cc_final: 0.7300 (t0)
REVERT: B  155 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6727 (tt)
REVERT: B  179 THR cc_start: 0.8224 (p) cc_final: 0.7950 (t)
REVERT: C   17 LYS cc_start: 0.8394 (mttm) cc_final: 0.8179 (mmtm)
REVERT: C   33 GLU cc_start: 0.7366 (tt0) cc_final: 0.7016 (tt0)
REVERT: C  197 LYS cc_start: 0.8009 (mttm) cc_final: 0.7627 (mttm)
REVERT: C  200 ASP cc_start: 0.8073 (t0) cc_final: 0.7766 (t0)
REVERT: C  245 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6943 (tm-30)
REVERT: C  277 LYS cc_start: 0.7312 (tttm) cc_final: 0.7001 (tttm)
REVERT: C  317 LYS cc_start: 0.7425 (mtmm) cc_final: 0.6879 (mtmt)
REVERT: D   52 VAL cc_start: 0.7738 (p) cc_final: 0.7358 (m)
REVERT: D   59 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7785 (pt)
  outliers start: 51
  outliers final: 46
  residues processed: 242
  average time/residue: 0.1003
  time to fit residues: 32.9913
Evaluate side-chains
  259 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 211
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 MET
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  109 SER
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  121 ASN
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  145 ARG
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  158 SER
Chi-restraints excluded: chain A residue  162 PHE
Chi-restraints excluded: chain A residue  172 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 ASP
Chi-restraints excluded: chain A residue  232 THR
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  285 THR
Chi-restraints excluded: chain A residue  288 SER
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   45 SER
Chi-restraints excluded: chain B residue  116 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  227 ILE
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  251 THR
Chi-restraints excluded: chain B residue  253 THR
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue  209 LYS
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  318 GLU
Chi-restraints excluded: chain C residue  341 ASP
Chi-restraints excluded: chain D residue   18 PHE
Chi-restraints excluded: chain D residue   59 LEU
Chi-restraints excluded: chain D residue   62 LEU
Chi-restraints excluded: chain D residue   65 LEU
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  151 TYR
Chi-restraints excluded: chain D residue  156 SER
Chi-restraints excluded: chain D residue  178 LEU
Chi-restraints excluded: chain D residue  186 LEU
Chi-restraints excluded: chain D residue  188 MET
Chi-restraints excluded: chain D residue  197 LEU
Chi-restraints excluded: chain D residue  220 ARG
Chi-restraints excluded: chain D residue  290 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   chunk 65 optimal weight:    0.0570
   chunk 39 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 36 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A 277 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.154420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.133569 restraints weight = 12996.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.18
r_work: 0.3526 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       57 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       58 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9025  Z= 0.132
  Angle     :  0.658  15.111  12232  Z= 0.322
  Chirality :  0.045   0.312   1382
  Planarity :  0.005   0.072   1544
  Dihedral  :  6.014  56.691   1262
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.15 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 32.15 %
    Favored  : 62.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.38 (0.25), residues: 1107
  helix:  1.16 (0.26), residues: 388
  sheet: -0.18 (0.31), residues: 262
  loop : -1.54 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  63 
 TYR   0.018   0.001   TYR B 228 
 PHE   0.033   0.002   PHE D 278 
 TRP   0.008   0.001   TRP D 140 
 HIS   0.003   0.001   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9022)
  covalent geometry    : angle       0.65774 (12226)
  SS BOND              : bond        0.00485 (    3)
  SS BOND              : angle       0.97004 (    6)
  hydrogen bonds       : bond        0.03280 (  396)
  hydrogen bonds       : angle       4.91925 ( 1143)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2301.96 seconds
wall clock time: 40 minutes 10.16 seconds (2410.16 seconds total)