Starting phenix.real_space_refine
on Wed Mar 12 04:18:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k4p_36889/03_2025/8k4p_36889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k4p_36889/03_2025/8k4p_36889.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k4p_36889/03_2025/8k4p_36889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k4p_36889/03_2025/8k4p_36889.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k4p_36889/03_2025/8k4p_36889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k4p_36889/03_2025/8k4p_36889.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.047
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: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    4600      2.51       5
     N    1250      2.21       5
     O    1327      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7231
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "A"
      Number of atoms: 2345
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2345
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 6, 'TRANS': 287}
    Chain: "C"
      Number of atoms: 1867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1867
          Classifications: {'peptide': 232}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 229}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
  Time building chain proxies: 4.93, per 1000 atoms: 0.68
  Number of scatterers: 7231
  At special positions: 0
  Unit cell: (78.2, 102.85, 136.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      54     16.00
     O    1327      8.00
     N    1250      7.00
     C    4600      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 118 " - pdb=" SG  CYS A 196 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1728

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      44.3% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'A' and resid 48 through 75
      removed outlier: 3.633A  pdb=" N   LEU A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   HIS A  75 " --> pdb=" O   ILE A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 91
      removed outlier: 3.657A  pdb=" N   ILE A  84 " --> pdb=" O   GLY A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
      removed outlier: 3.693A  pdb=" N   LEU A  96 " --> pdb=" O   ASN A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 149
      removed outlier: 4.024A  pdb=" N   CYS A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ARG A 119 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   PHE A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ASP A 132 " --> pdb=" O   TYR A 128 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE A 133 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   CYS A 138 " --> pdb=" O   PHE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 183
      removed outlier: 4.305A  pdb=" N   GLY A 161 " --> pdb=" O   LYS A 157 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A 169 " --> pdb=" O   THR A 165 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG A 181 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   HIS A 182 " --> pdb=" O   ASP A 178 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ARG A 183 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 220
    Processing helix  chain 'A' and resid 221 through 239
      removed outlier: 3.626A  pdb=" N   VAL A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 279
      removed outlier: 3.815A  pdb=" N   GLY A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      Proline residue:  A 266  - end of helix
    Processing helix  chain 'A' and resid 287 through 318
      removed outlier: 3.789A  pdb=" N   LEU A 291 " --> pdb=" O   TYR A 287 " (cutoff:3.500A)
      Proline residue:  A 311  - end of helix
      removed outlier: 4.025A  pdb=" N   GLY A 318 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 336
      removed outlier: 3.520A  pdb=" N   ARG A 333 " --> pdb=" O   PHE A 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 31
      removed outlier: 3.659A  pdb=" N   ALA C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ALA C  12 " --> pdb=" O   GLU C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 53
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 3.529A  pdb=" N   LYS C 210 " --> pdb=" O   GLU C 207 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU C 216 " --> pdb=" O   HIS C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 255
      removed outlier: 3.739A  pdb=" N   GLU C 245 " --> pdb=" O   ASN C 241 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   SER C 246 " --> pdb=" O   ARG C 242 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 275
    Processing helix  chain 'C' and resid 276 through 281
    Processing helix  chain 'C' and resid 295 through 309
      removed outlier: 4.195A  pdb=" N   TYR C 302 " --> pdb=" O   GLU C 298 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE C 303 " --> pdb=" O   ALA C 299 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS C 305 " --> pdb=" O   ALA C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 351
      removed outlier: 3.875A  pdb=" N   ASP C 341 " --> pdb=" O   ASP C 337 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   VAL C 342 " --> pdb=" O   ALA C 338 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ILE C 344 " --> pdb=" O   THR C 340 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 24
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.512A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.862A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.656A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.871A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.658A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.136A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.551A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.961A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.647A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.790A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 190
      removed outlier: 6.249A  pdb=" N   VAL C  34 " --> pdb=" O   LYS C 197 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   PHE C 199 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU C  36 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 8.187A  pdb=" N   VAL C 201 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   LEU C  38 " --> pdb=" O   VAL C 201 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA C 220 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1020 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: 1.91

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1363
        1.33 -     1.45: 1837
        1.45 -     1.58: 4093
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 7367
  Sorted by residual:
  bond pdb=" CA  ARG C  24 "
       pdb=" C   ARG C  24 "
    ideal  model  delta    sigma   weight residual
    1.523  1.481  0.042 1.37e-02 5.33e+03 9.33e+00
  bond pdb=" CA  MET C  18 "
       pdb=" CB  MET C  18 "
    ideal  model  delta    sigma   weight residual
    1.528  1.482  0.046 1.66e-02 3.63e+03 7.70e+00
  bond pdb=" CA  LYS C 280 "
       pdb=" C   LYS C 280 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.018 7.00e-03 2.04e+04 6.89e+00
  bond pdb=" C   MET C  18 "
       pdb=" O   MET C  18 "
    ideal  model  delta    sigma   weight residual
    1.236  1.203  0.033 1.26e-02 6.30e+03 6.81e+00
  bond pdb=" C   ARG C  24 "
       pdb=" O   ARG C  24 "
    ideal  model  delta    sigma   weight residual
    1.236  1.203  0.034 1.29e-02 6.01e+03 6.77e+00
  ... (remaining 7362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 9736
        1.61 -     3.23: 189
        3.23 -     4.84: 33
        4.84 -     6.46: 7
        6.46 -     8.07: 4
  Bond angle restraints: 9969
  Sorted by residual:
  angle pdb=" N   ARG A 185 "
        pdb=" CA  ARG A 185 "
        pdb=" C   ARG A 185 "
      ideal   model   delta    sigma   weight residual
     110.43  103.69    6.74 1.31e+00 5.83e-01 2.65e+01
  angle pdb=" C   SER A 285 "
        pdb=" N   CYS A 286 "
        pdb=" CA  CYS A 286 "
      ideal   model   delta    sigma   weight residual
     121.54  128.44   -6.90 1.91e+00 2.74e-01 1.31e+01
  angle pdb=" C   LYS C 280 "
        pdb=" CA  LYS C 280 "
        pdb=" CB  LYS C 280 "
      ideal   model   delta    sigma   weight residual
     111.65  106.72    4.93 1.44e+00 4.82e-01 1.17e+01
  angle pdb=" O   LEU C  23 "
        pdb=" C   LEU C  23 "
        pdb=" N   ARG C  24 "
      ideal   model   delta    sigma   weight residual
     122.12  118.92    3.20 1.06e+00 8.90e-01 9.13e+00
  angle pdb=" CA  ILE A 282 "
        pdb=" CB  ILE A 282 "
        pdb=" CG1 ILE A 282 "
      ideal   model   delta    sigma   weight residual
     110.40  115.28   -4.88 1.70e+00 3.46e-01 8.23e+00
  ... (remaining 9964 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 3707
       17.13 -    34.26: 504
       34.26 -    51.38: 140
       51.38 -    68.51: 32
       68.51 -    85.64: 12
  Dihedral angle restraints: 4395
    sinusoidal: 1724
      harmonic: 2671
  Sorted by residual:
  dihedral pdb=" CA  LEU C 268 "
           pdb=" C   LEU C 268 "
           pdb=" N   ASN C 269 "
           pdb=" CA  ASN C 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.83  -22.17     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  MET A 195 "
           pdb=" C   MET A 195 "
           pdb=" N   CYS A 196 "
           pdb=" CA  CYS A 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.43   19.57     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" CA  ILE A 112 "
           pdb=" C   ILE A 112 "
           pdb=" N   ILE A 113 "
           pdb=" CA  ILE A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.65  -19.35     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 4392 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 801
       0.038 -    0.076: 262
       0.076 -    0.114: 70
       0.114 -    0.151: 15
       0.151 -    0.189: 1
  Chirality restraints: 1149
  Sorted by residual:
  chirality pdb=" CA  VAL A 310 "
            pdb=" N   VAL A 310 "
            pdb=" C   VAL A 310 "
            pdb=" CB  VAL A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.25    0.19 2.00e-01 2.50e+01 8.96e-01
  chirality pdb=" CA  TRP A 154 "
            pdb=" N   TRP A 154 "
            pdb=" C   TRP A 154 "
            pdb=" CB  TRP A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.14e-01
  chirality pdb=" CA  ILE C 265 "
            pdb=" N   ILE C 265 "
            pdb=" C   ILE C 265 "
            pdb=" CB  ILE C 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1146 not shown)

  Planarity restraints: 1255
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 310 "    0.041 5.00e-02 4.00e+02   6.14e-02 6.03e+00
        pdb=" N   PRO A 311 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 311 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 311 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO B 236 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 242 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.66e+00
        pdb=" C   LYS A 242 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LYS A 242 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 243 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1252 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 124
        2.68 -     3.23: 6676
        3.23 -     3.79: 10460
        3.79 -     4.34: 14814
        4.34 -     4.90: 24949
  Nonbonded interactions: 57023
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  99 "
            pdb=" OE2 GLU A 121 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" OD1 ASN A  61 "
            pdb=" OG  SER A  93 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ALA A 172 "
            pdb=" OG  SER A 176 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NH1 ARG A 183 "
            pdb=" O   CYS A 196 "
     model   vdw
     2.246 3.120
  ... (remaining 57018 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=1.00 max=1.00 mean=1.00
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:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.140
  Find NCS groups from input model:        0.080
  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:13.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
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      :  0.003   0.046   7367  Z= 0.198
  Angle     :  0.579   8.070   9969  Z= 0.325
  Chirality :  0.041   0.189   1149
  Planarity :  0.004   0.061   1255
  Dihedral  : 17.491  85.640   2664
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 27.88 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.27), residues: 908
  helix:  1.07 (0.27), residues: 369
  sheet:  1.15 (0.38), residues: 174
  loop : -1.66 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 210 
 PHE   0.013   0.001   PHE A 329 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.006   0.000   ARG A 208 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 MET cc_start: 0.4125 (ttt) cc_final: 0.3760 (ppp)
REVERT: C   18 MET cc_start: 0.7522 (ttp) cc_final: 0.7259 (ttp)
REVERT: C   24 ARG cc_start: 0.7550 (ptm160) cc_final: 0.7175 (ptp90)
REVERT: C   29 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7482 (tttm)
  outliers start: 20
  outliers final: 17
  residues processed: 106
  average time/residue: 1.3295
  time to fit residues: 148.3016
Evaluate side-chains
  101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  180 CYS
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  307 SER
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  260 THR
Chi-restraints excluded: chain C residue  315 ASP
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain C residue  332 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 37 optimal weight:    6.9990
   chunk 23 optimal weight:    0.5980
   chunk 46 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.174670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.122759 restraints weight = 8008.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.25
r_work: 0.3323 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7367  Z= 0.196
  Angle     :  0.529   6.730   9969  Z= 0.283
  Chirality :  0.041   0.165   1149
  Planarity :  0.004   0.045   1255
  Dihedral  :  5.795  58.049   1023
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 22.56 %
    Favored  : 71.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.27), residues: 908
  helix:  1.65 (0.27), residues: 384
  sheet:  1.20 (0.39), residues: 171
  loop : -1.88 (0.27), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 182 
 PHE   0.015   0.001   PHE A 134 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.005   0.000   ARG A 183 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 89
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
REVERT: B  226 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7888 (mm-30)
REVERT: A  106 MET cc_start: 0.6656 (tpt) cc_final: 0.6263 (tmm)
REVERT: A  175 LEU cc_start: 0.7554 (mt) cc_final: 0.7302 (mt)
REVERT: A  190 VAL cc_start: 0.2278 (OUTLIER) cc_final: 0.1937 (t)
REVERT: A  203 MET cc_start: 0.4213 (ttt) cc_final: 0.3821 (ppp)
REVERT: A  212 ARG cc_start: 0.6755 (mmm-85) cc_final: 0.6555 (mmm-85)
REVERT: A  273 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7082 (tt)
REVERT: C   18 MET cc_start: 0.7610 (ttp) cc_final: 0.7277 (tmm)
REVERT: C   20 ASP cc_start: 0.8227 (t0) cc_final: 0.7448 (m-30)
REVERT: C   24 ARG cc_start: 0.7386 (ptm160) cc_final: 0.6948 (ptp90)
REVERT: C  233 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7481 (p)
REVERT: C  240 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.5053 (ttt)
  outliers start: 48
  outliers final: 16
  residues processed: 124
  average time/residue: 1.1112
  time to fit residues: 146.0735
Evaluate side-chains
  102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  240 MET
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  327 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:   10.0000
   chunk 85 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 86 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 303 GLN
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 255 ASN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.173234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.120730 restraints weight = 8186.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.28
r_work: 0.3305 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7367  Z= 0.199
  Angle     :  0.513   6.559   9969  Z= 0.275
  Chirality :  0.041   0.180   1149
  Planarity :  0.003   0.043   1255
  Dihedral  :  5.470  59.008   1010
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 22.18 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.28), residues: 908
  helix:  1.97 (0.28), residues: 385
  sheet:  1.18 (0.39), residues: 166
  loop : -1.92 (0.27), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 182 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.003   0.000   ARG A 183 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 82
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8072 (mt0)
REVERT: B  226 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7878 (mm-30)
REVERT: A  106 MET cc_start: 0.6694 (tpt) cc_final: 0.6189 (tmm)
REVERT: A  175 LEU cc_start: 0.7483 (mt) cc_final: 0.7250 (mt)
REVERT: A  190 VAL cc_start: 0.1975 (OUTLIER) cc_final: 0.1631 (t)
REVERT: A  203 MET cc_start: 0.4443 (ttt) cc_final: 0.3897 (ppp)
REVERT: A  273 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7161 (tt)
REVERT: C   18 MET cc_start: 0.7773 (ttp) cc_final: 0.7344 (tmm)
REVERT: C   24 ARG cc_start: 0.7328 (ptm160) cc_final: 0.6888 (ptp90)
REVERT: C  233 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7488 (p)
REVERT: C  279 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7143 (mptt)
  outliers start: 46
  outliers final: 21
  residues processed: 114
  average time/residue: 1.1754
  time to fit residues: 141.7521
Evaluate side-chains
  109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0980
   chunk 17 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.173934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.127997 restraints weight = 8180.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 2.21
r_work: 0.3310 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7367  Z= 0.190
  Angle     :  0.502   6.636   9969  Z= 0.269
  Chirality :  0.040   0.167   1149
  Planarity :  0.003   0.042   1255
  Dihedral  :  5.432  57.497   1010
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 21.80 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 908
  helix:  2.10 (0.28), residues: 385
  sheet:  1.20 (0.39), residues: 166
  loop : -1.93 (0.27), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 182 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.002   0.000   ARG A 212 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 84
  time to evaluate  : 0.794 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8251 (mt0)
REVERT: B  325 MET cc_start: 0.8978 (mmt) cc_final: 0.8576 (mmt)
REVERT: B  336 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8490 (mt)
REVERT: A  106 MET cc_start: 0.6833 (tpt) cc_final: 0.6326 (tmm)
REVERT: A  175 LEU cc_start: 0.7537 (mt) cc_final: 0.7294 (mt)
REVERT: A  183 ARG cc_start: 0.5058 (ttm-80) cc_final: 0.4401 (ttm170)
REVERT: A  190 VAL cc_start: 0.1594 (OUTLIER) cc_final: 0.1316 (t)
REVERT: A  203 MET cc_start: 0.4208 (ttt) cc_final: 0.3856 (ppp)
REVERT: C   18 MET cc_start: 0.7948 (ttp) cc_final: 0.7534 (tmm)
REVERT: C   24 ARG cc_start: 0.7450 (ptm160) cc_final: 0.7061 (ptp90)
REVERT: C  233 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7605 (p)
REVERT: C  279 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7360 (mtpt)
  outliers start: 48
  outliers final: 22
  residues processed: 119
  average time/residue: 1.2288
  time to fit residues: 154.3894
Evaluate side-chains
  109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 82
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0370
   chunk 57 optimal weight:    0.0470
   chunk 7 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 255 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.176809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.131566 restraints weight = 8080.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.19
r_work: 0.3364 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7367  Z= 0.131
  Angle     :  0.458   6.679   9969  Z= 0.245
  Chirality :  0.039   0.149   1149
  Planarity :  0.003   0.041   1255
  Dihedral  :  5.181  55.076   1010
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.19 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.28), residues: 908
  helix:  2.34 (0.28), residues: 384
  sheet:  1.28 (0.39), residues: 167
  loop : -1.82 (0.28), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 182 
 PHE   0.012   0.001   PHE C 189 
 TYR   0.008   0.001   TYR B 124 
 ARG   0.002   0.000   ARG A 212 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 83
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
REVERT: B   47 THR cc_start: 0.8968 (t) cc_final: 0.8615 (m)
REVERT: B  325 MET cc_start: 0.8928 (mmt) cc_final: 0.8534 (mmt)
REVERT: A   56 LEU cc_start: 0.8126 (mp) cc_final: 0.7919 (mp)
REVERT: A  106 MET cc_start: 0.6681 (tpt) cc_final: 0.6241 (tmm)
REVERT: A  175 LEU cc_start: 0.7396 (mt) cc_final: 0.7165 (mt)
REVERT: A  183 ARG cc_start: 0.5071 (ttm-80) cc_final: 0.4601 (ttm170)
REVERT: A  190 VAL cc_start: 0.1672 (OUTLIER) cc_final: 0.1397 (t)
REVERT: A  203 MET cc_start: 0.4349 (ttt) cc_final: 0.3814 (ppp)
REVERT: C   18 MET cc_start: 0.7869 (ttp) cc_final: 0.7473 (tmm)
REVERT: C   24 ARG cc_start: 0.7383 (ptm160) cc_final: 0.7001 (ptp90)
REVERT: C  184 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8388 (tp)
REVERT: C  233 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7523 (p)
REVERT: C  279 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7339 (mtpt)
  outliers start: 37
  outliers final: 14
  residues processed: 111
  average time/residue: 1.2426
  time to fit residues: 145.9859
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  208 ARG
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.172102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.119982 restraints weight = 8157.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.23
r_work: 0.3280 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7367  Z= 0.272
  Angle     :  0.540   6.972   9969  Z= 0.285
  Chirality :  0.042   0.178   1149
  Planarity :  0.004   0.041   1255
  Dihedral  :  5.049  53.497   1007
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 22.18 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.28), residues: 908
  helix:  2.19 (0.28), residues: 385
  sheet:  1.18 (0.39), residues: 161
  loop : -1.94 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 182 
 PHE   0.016   0.002   PHE C 189 
 TYR   0.013   0.001   TYR A 128 
 ARG   0.002   0.000   ARG A 119 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 83
  time to evaluate  : 0.892 
Fit side-chains
REVERT: B  146 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8969 (mp)
REVERT: B  336 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8464 (mt)
REVERT: A  106 MET cc_start: 0.6783 (tpt) cc_final: 0.6322 (tmm)
REVERT: A  175 LEU cc_start: 0.7275 (mt) cc_final: 0.7058 (mt)
REVERT: A  183 ARG cc_start: 0.5073 (ttm-80) cc_final: 0.4575 (ttm170)
REVERT: A  190 VAL cc_start: 0.1720 (OUTLIER) cc_final: 0.1464 (t)
REVERT: A  203 MET cc_start: 0.4258 (ttt) cc_final: 0.3824 (ppp)
REVERT: A  242 LYS cc_start: 0.8079 (tttt) cc_final: 0.7875 (tttm)
REVERT: A  247 ARG cc_start: 0.8056 (ptm160) cc_final: 0.7248 (mtm-85)
REVERT: C   18 MET cc_start: 0.7834 (ttp) cc_final: 0.7389 (tmm)
REVERT: C   24 ARG cc_start: 0.7396 (ptm160) cc_final: 0.6943 (ptp90)
REVERT: C  233 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7448 (p)
REVERT: C  249 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8082 (tt)
REVERT: C  279 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7322 (mtpt)
  outliers start: 45
  outliers final: 20
  residues processed: 117
  average time/residue: 1.8224
  time to fit residues: 225.9344
Evaluate side-chains
  105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0270
   chunk 79 optimal weight:    7.9990
   chunk 54 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0170
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.174786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.129608 restraints weight = 8079.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 2.16
r_work: 0.3344 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7367  Z= 0.153
  Angle     :  0.481   7.221   9969  Z= 0.255
  Chirality :  0.039   0.157   1149
  Planarity :  0.003   0.047   1255
  Dihedral  :  4.400  45.928   1003
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.95 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.28), residues: 908
  helix:  2.33 (0.28), residues: 385
  sheet:  1.23 (0.39), residues: 162
  loop : -1.90 (0.27), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 182 
 PHE   0.013   0.001   PHE C 189 
 TYR   0.009   0.001   TYR A 128 
 ARG   0.005   0.000   ARG A 208 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 83
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: B  146 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8961 (mp)
REVERT: B  325 MET cc_start: 0.8968 (mmt) cc_final: 0.8580 (mmt)
REVERT: A   56 LEU cc_start: 0.8146 (mp) cc_final: 0.7939 (mp)
REVERT: A  106 MET cc_start: 0.6648 (tpt) cc_final: 0.6291 (tmm)
REVERT: A  175 LEU cc_start: 0.7420 (mt) cc_final: 0.7102 (mp)
REVERT: A  183 ARG cc_start: 0.5133 (ttm-80) cc_final: 0.4616 (ttm170)
REVERT: A  190 VAL cc_start: 0.1702 (OUTLIER) cc_final: 0.1436 (t)
REVERT: A  203 MET cc_start: 0.4369 (ttt) cc_final: 0.3849 (ppp)
REVERT: A  242 LYS cc_start: 0.8128 (tttt) cc_final: 0.7910 (tttm)
REVERT: A  333 ARG cc_start: 0.6107 (OUTLIER) cc_final: 0.5076 (tpt170)
REVERT: C   18 MET cc_start: 0.7880 (ttp) cc_final: 0.7491 (tmm)
REVERT: C   24 ARG cc_start: 0.7374 (ptm160) cc_final: 0.6997 (ptp90)
REVERT: C  233 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7484 (p)
REVERT: C  249 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8165 (tt)
REVERT: C  279 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7435 (mtpt)
  outliers start: 32
  outliers final: 18
  residues processed: 107
  average time/residue: 1.2040
  time to fit residues: 135.9228
Evaluate side-chains
  105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0000
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0270
   chunk 30 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 85 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.0048

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.172985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.121215 restraints weight = 8223.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.24
r_work: 0.3297 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7367  Z= 0.217
  Angle     :  0.515   6.952   9969  Z= 0.272
  Chirality :  0.041   0.176   1149
  Planarity :  0.003   0.040   1255
  Dihedral  :  4.471  41.846   1003
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 23.07 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.28), residues: 908
  helix:  2.27 (0.28), residues: 385
  sheet:  1.15 (0.39), residues: 161
  loop : -1.94 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 182 
 PHE   0.015   0.001   PHE C 189 
 TYR   0.012   0.001   TYR A 128 
 ARG   0.003   0.000   ARG A 208 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 79
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: B  146 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8944 (mp)
REVERT: B  301 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6811 (mtpt)
REVERT: B  336 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8463 (mt)
REVERT: A  106 MET cc_start: 0.6729 (tpt) cc_final: 0.6318 (tmm)
REVERT: A  175 LEU cc_start: 0.7209 (mt) cc_final: 0.6849 (mp)
REVERT: A  183 ARG cc_start: 0.5097 (ttm-80) cc_final: 0.4445 (ttm170)
REVERT: A  190 VAL cc_start: 0.1601 (OUTLIER) cc_final: 0.1356 (t)
REVERT: A  203 MET cc_start: 0.4298 (ttt) cc_final: 0.3628 (ppp)
REVERT: A  242 LYS cc_start: 0.8097 (tttt) cc_final: 0.7846 (tttm)
REVERT: A  333 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.4980 (tpt170)
REVERT: C   18 MET cc_start: 0.7809 (ttp) cc_final: 0.7370 (tmm)
REVERT: C   24 ARG cc_start: 0.7335 (ptm160) cc_final: 0.6932 (ptp90)
REVERT: C  233 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7420 (p)
REVERT: C  249 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8062 (tt)
REVERT: C  279 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7376 (mtpt)
  outliers start: 40
  outliers final: 25
  residues processed: 110
  average time/residue: 1.7954
  time to fit residues: 208.0498
Evaluate side-chains
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  337 MET
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  298 GLU
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 89 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0670
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0370
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.175396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.130269 restraints weight = 8194.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.17
r_work: 0.3356 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7367  Z= 0.140
  Angle     :  0.468   7.001   9969  Z= 0.248
  Chirality :  0.039   0.162   1149
  Planarity :  0.003   0.040   1255
  Dihedral  :  4.203  41.677   1003
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.21 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.28), residues: 908
  helix:  2.45 (0.28), residues: 385
  sheet:  1.17 (0.38), residues: 168
  loop : -1.89 (0.28), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 182 
 PHE   0.013   0.001   PHE C 189 
 TYR   0.008   0.001   TYR B 124 
 ARG   0.002   0.000   ARG A 208 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 1.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  146 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8934 (mp)
REVERT: B  217 MET cc_start: 0.8665 (pmt) cc_final: 0.8283 (pmm)
REVERT: B  325 MET cc_start: 0.8961 (mmt) cc_final: 0.8581 (mmt)
REVERT: A   56 LEU cc_start: 0.8127 (mp) cc_final: 0.7927 (mp)
REVERT: A  106 MET cc_start: 0.6752 (tpt) cc_final: 0.6350 (tmm)
REVERT: A  175 LEU cc_start: 0.7329 (mt) cc_final: 0.7012 (mp)
REVERT: A  183 ARG cc_start: 0.5187 (ttm-80) cc_final: 0.4715 (ttm170)
REVERT: A  190 VAL cc_start: 0.1693 (OUTLIER) cc_final: 0.1401 (t)
REVERT: A  203 MET cc_start: 0.4332 (ttt) cc_final: 0.3685 (ppp)
REVERT: A  242 LYS cc_start: 0.8171 (tttt) cc_final: 0.7936 (tttm)
REVERT: A  333 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5078 (tpt170)
REVERT: C   18 MET cc_start: 0.7858 (ttp) cc_final: 0.7475 (tmm)
REVERT: C   24 ARG cc_start: 0.7429 (ptm160) cc_final: 0.7057 (ptp90)
REVERT: C  233 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7459 (p)
REVERT: C  249 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8193 (tt)
REVERT: C  279 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7449 (mtpt)
  outliers start: 32
  outliers final: 20
  residues processed: 103
  average time/residue: 1.6183
  time to fit residues: 175.8882
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  337 MET
Chi-restraints excluded: chain C residue  198 MET
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  279 LYS
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 49 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.4050 r_free = 0.4050 target = 0.170353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.124858 restraints weight = 8312.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.30
r_work: 0.3258 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7367  Z= 0.347
  Angle     :  0.582   8.010   9969  Z= 0.306
  Chirality :  0.044   0.200   1149
  Planarity :  0.004   0.042   1255
  Dihedral  :  4.716  40.504   1003
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 24.71 %
    Favored  : 71.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.28), residues: 908
  helix:  2.09 (0.28), residues: 385
  sheet:  1.19 (0.39), residues: 160
  loop : -1.96 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.003   0.001   HIS C 213 
 PHE   0.017   0.002   PHE C 189 
 TYR   0.015   0.001   TYR A 128 
 ARG   0.003   0.000   ARG A 208 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: B  146 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8974 (mp)
REVERT: A  106 MET cc_start: 0.6825 (tpt) cc_final: 0.6362 (tmm)
REVERT: A  175 LEU cc_start: 0.7369 (mt) cc_final: 0.7014 (mp)
REVERT: A  183 ARG cc_start: 0.5152 (ttm-80) cc_final: 0.4667 (ttm170)
REVERT: A  190 VAL cc_start: 0.1431 (OUTLIER) cc_final: 0.1155 (t)
REVERT: A  203 MET cc_start: 0.4166 (ttt) cc_final: 0.3481 (ppp)
REVERT: A  242 LYS cc_start: 0.8155 (tttt) cc_final: 0.7946 (tttm)
REVERT: A  333 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5191 (tpt170)
REVERT: C   18 MET cc_start: 0.7995 (ttp) cc_final: 0.7590 (tmm)
REVERT: C   24 ARG cc_start: 0.7564 (ptm160) cc_final: 0.7131 (ptp90)
REVERT: C  233 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7497 (p)
REVERT: C  249 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8224 (tt)
  outliers start: 30
  outliers final: 22
  residues processed: 102
  average time/residue: 1.2084
  time to fit residues: 130.2371
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  333 ARG
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain C residue  206 SER
Chi-restraints excluded: chain C residue  233 VAL
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  327 THR
Chi-restraints excluded: chain C residue  332 VAL
Chi-restraints excluded: chain C residue  354 PHE
Chi-restraints excluded: chain G residue   37 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0670
   chunk 17 optimal weight:    0.2980
   chunk 50 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.173718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121758 restraints weight = 8158.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.27
r_work: 0.3313 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7367  Z= 0.164
  Angle     :  0.486   6.978   9969  Z= 0.258
  Chirality :  0.040   0.189   1149
  Planarity :  0.003   0.040   1255
  Dihedral  :  4.339  42.250   1003
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.84 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 908
  helix:  2.32 (0.28), residues: 385
  sheet:  1.15 (0.39), residues: 168
  loop : -1.95 (0.27), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A 182 
 PHE   0.019   0.001   PHE B 292 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.002   0.000   ARG A 208 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 6624.26 seconds
wall clock time: 117 minutes 38.44 seconds (7058.44 seconds total)