Starting phenix.real_space_refine
on Sun May 11 01:35:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k4p_36889/05_2025/8k4p_36889.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k4p_36889/05_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_36889/05_2025/8k4p_36889.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k4p_36889/05_2025/8k4p_36889.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k4p_36889/05_2025/8k4p_36889.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k4p_36889/05_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-5687/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: 5.09, per 1000 atoms: 0.70
  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: 1.75
  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: 0.84
  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: 1.95

  Time building geometry restraints manager: 2.06 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:             1.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.420
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:11.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.420
-------------------------------------------------------------------------------
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   7368  Z= 0.158
  Angle     :  0.580   8.070   9971  Z= 0.326
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17358 (  348)
  hydrogen bonds       : angle       5.95712 ( 1020)
  SS BOND              : bond        0.00931 (    1)
  SS BOND              : angle       2.27828 (    2)
  covalent geometry    : bond        0.00291 ( 7367)
  covalent geometry    : angle       0.57933 ( 9969)

*********************** 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  : 0.742 
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: 1.2752
  time to fit residues: 142.1093
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  : 0.838 
-------------------------------------------------------------------------------
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 = 52)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.122746 restraints weight = 8008.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.25
r_work: 0.3323 rms_B_bonded: 2.92 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: 0.8359
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   7368  Z= 0.127
  Angle     :  0.530   6.730   9971  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04514 (  348)
  hydrogen bonds       : angle       3.96234 ( 1020)
  SS BOND              : bond        0.01017 (    1)
  SS BOND              : angle       2.58883 (    2)
  covalent geometry    : bond        0.00288 ( 7367)
  covalent geometry    : angle       0.52910 ( 9969)

*********************** 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  : 0.915 
Fit side-chains
   revert: symmetry clash
REVERT: B  226 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7898 (mm-30)
REVERT: A  106 MET cc_start: 0.6662 (tpt) cc_final: 0.6266 (tmm)
REVERT: A  175 LEU cc_start: 0.7552 (mt) cc_final: 0.7299 (mt)
REVERT: A  190 VAL cc_start: 0.2279 (OUTLIER) cc_final: 0.1936 (t)
REVERT: A  203 MET cc_start: 0.4220 (ttt) cc_final: 0.3828 (ppp)
REVERT: A  212 ARG cc_start: 0.6758 (mmm-85) cc_final: 0.6557 (mmm-85)
REVERT: A  273 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7088 (tt)
REVERT: C   18 MET cc_start: 0.7615 (ttp) cc_final: 0.7282 (tmm)
REVERT: C   20 ASP cc_start: 0.8230 (t0) cc_final: 0.7453 (m-30)
REVERT: C   24 ARG cc_start: 0.7390 (ptm160) cc_final: 0.6953 (ptp90)
REVERT: C  233 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7483 (p)
REVERT: C  240 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.5061 (ttt)
  outliers start: 48
  outliers final: 16
  residues processed: 124
  average time/residue: 1.1434
  time to fit residues: 149.9183
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  : 0.733 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 85 optimal weight:    8.9990
   chunk 76 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 86 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0870
   overall best weight:    0.9760

-------------------------------------------------------------------------------
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 = 0.4069 r_free = 0.4069 target = 0.172738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.120235 restraints weight = 8190.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.28
r_work: 0.3296 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7368  Z= 0.141
  Angle     :  0.525   6.514   9971  Z= 0.281
  Chirality :  0.041   0.180   1149
  Planarity :  0.004   0.042   1255
  Dihedral  :  5.514  59.893   1010
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  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:  0.53 (0.27), residues: 908
  helix:  1.92 (0.28), residues: 385
  sheet:  1.17 (0.39), residues: 166
  loop : -1.94 (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   0.015   0.001   PHE A  72 
 TYR   0.011   0.001   TYR A 128 
 ARG   0.003   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04625 (  348)
  hydrogen bonds       : angle       3.83747 ( 1020)
  SS BOND              : bond        0.00875 (    1)
  SS BOND              : angle       2.26843 (    2)
  covalent geometry    : bond        0.00326 ( 7367)
  covalent geometry    : angle       0.52443 ( 9969)

*********************** 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
  127 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 81
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8071 (mt0)
REVERT: B  226 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7887 (mm-30)
REVERT: A  106 MET cc_start: 0.6700 (tpt) cc_final: 0.6190 (tmm)
REVERT: A  175 LEU cc_start: 0.7482 (mt) cc_final: 0.7254 (mt)
REVERT: A  190 VAL cc_start: 0.2032 (OUTLIER) cc_final: 0.1689 (t)
REVERT: A  203 MET cc_start: 0.4413 (ttt) cc_final: 0.3896 (ppp)
REVERT: A  273 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7091 (tt)
REVERT: C   18 MET cc_start: 0.7780 (ttp) cc_final: 0.7349 (tmm)
REVERT: C   24 ARG cc_start: 0.7431 (ptm160) cc_final: 0.6986 (ptp90)
REVERT: C  233 VAL cc_start: 0.7837 (OUTLIER) cc_final: 0.7519 (p)
  outliers start: 46
  outliers final: 21
  residues processed: 113
  average time/residue: 1.2082
  time to fit residues: 144.6047
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  : 0.806 
-------------------------------------------------------------------------------
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  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:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0970
   chunk 60 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.175364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.131071 restraints weight = 8223.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.26
r_work: 0.3333 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7368  Z= 0.136
  Angle     :  0.512   6.670   9971  Z= 0.274
  Chirality :  0.041   0.166   1149
  Planarity :  0.004   0.042   1255
  Dihedral  :  5.470  55.519   1010
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 21.67 %
    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:  0.60 (0.28), residues: 908
  helix:  2.03 (0.28), residues: 385
  sheet:  1.16 (0.39), residues: 166
  loop : -1.96 (0.27), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 182 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.011   0.001   TYR A 128 
 ARG   0.002   0.000   ARG A 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04369 (  348)
  hydrogen bonds       : angle       3.81581 ( 1020)
  SS BOND              : bond        0.00855 (    1)
  SS BOND              : angle       2.23703 (    2)
  covalent geometry    : bond        0.00314 ( 7367)
  covalent geometry    : angle       0.51113 ( 9969)

*********************** 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
  135 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 86
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8229 (mt0)
REVERT: B  336 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8459 (mt)
REVERT: A  106 MET cc_start: 0.6853 (tpt) cc_final: 0.6344 (tmm)
REVERT: A  175 LEU cc_start: 0.7583 (mt) cc_final: 0.7356 (mt)
REVERT: A  183 ARG cc_start: 0.5053 (ttm-80) cc_final: 0.4397 (ttm170)
REVERT: A  190 VAL cc_start: 0.1603 (OUTLIER) cc_final: 0.1328 (t)
REVERT: A  203 MET cc_start: 0.4171 (ttt) cc_final: 0.3807 (ppp)
REVERT: A  247 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7349 (mtm-85)
REVERT: C   18 MET cc_start: 0.7971 (ttp) cc_final: 0.7585 (tmm)
REVERT: C   24 ARG cc_start: 0.7498 (ptm160) cc_final: 0.7117 (ptp90)
REVERT: C  233 VAL cc_start: 0.7861 (OUTLIER) cc_final: 0.7540 (p)
REVERT: C  279 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7328 (mtpt)
  outliers start: 49
  outliers final: 23
  residues processed: 122
  average time/residue: 1.1997
  time to fit residues: 154.5126
Evaluate side-chains
  110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
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   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  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 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  340 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:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0770
   chunk 57 optimal weight:    0.0050
   chunk 7 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5352

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.175023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.129109 restraints weight = 8049.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 2.28
r_work: 0.3486 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7368  Z= 0.102
  Angle     :  0.474   6.733   9971  Z= 0.253
  Chirality :  0.039   0.149   1149
  Planarity :  0.003   0.041   1255
  Dihedral  :  4.959  53.910   1008
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.45 %
    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:  0.77 (0.28), residues: 908
  helix:  2.24 (0.28), residues: 385
  sheet:  1.32 (0.39), residues: 161
  loop : -1.94 (0.27), residues: 362

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   0.013   0.001   PHE C 189 
 TYR   0.008   0.001   TYR A 128 
 ARG   0.002   0.000   ARG A 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  348)
  hydrogen bonds       : angle       3.61227 ( 1020)
  SS BOND              : bond        0.00705 (    1)
  SS BOND              : angle       2.00243 (    2)
  covalent geometry    : bond        0.00220 ( 7367)
  covalent geometry    : angle       0.47293 ( 9969)

*********************** 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
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.7990 (mp) cc_final: 0.7780 (mp)
REVERT: A  106 MET cc_start: 0.6653 (tpt) cc_final: 0.6207 (tmm)
REVERT: A  175 LEU cc_start: 0.7019 (mt) cc_final: 0.6803 (mt)
REVERT: A  183 ARG cc_start: 0.4958 (ttm-80) cc_final: 0.4484 (ttm170)
REVERT: A  190 VAL cc_start: 0.1683 (OUTLIER) cc_final: 0.1410 (t)
REVERT: A  203 MET cc_start: 0.4347 (ttt) cc_final: 0.3808 (ppp)
REVERT: C   18 MET cc_start: 0.7283 (ttp) cc_final: 0.6839 (tmm)
REVERT: C   24 ARG cc_start: 0.6873 (ptm160) cc_final: 0.6459 (ptp90)
REVERT: C  233 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7441 (p)
REVERT: C  279 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7160 (mtpt)
  outliers start: 37
  outliers final: 17
  residues processed: 111
  average time/residue: 1.2421
  time to fit residues: 145.2637
Evaluate side-chains
  99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
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  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  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  237 VAL
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  277 LEU
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 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:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 88 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0970
   chunk 35 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.175631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.131147 restraints weight = 8185.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 2.26
r_work: 0.3336 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7368  Z= 0.133
  Angle     :  0.511   6.578   9971  Z= 0.271
  Chirality :  0.041   0.166   1149
  Planarity :  0.003   0.041   1255
  Dihedral  :  4.947  53.143   1007
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 22.69 %
    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:  0.74 (0.28), residues: 908
  helix:  2.23 (0.28), residues: 386
  sheet:  1.25 (0.39), residues: 160
  loop : -1.96 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 182 
 PHE   0.015   0.001   PHE C 189 
 TYR   0.012   0.001   TYR A 128 
 ARG   0.002   0.000   ARG A 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04212 (  348)
  hydrogen bonds       : angle       3.74205 ( 1020)
  SS BOND              : bond        0.00783 (    1)
  SS BOND              : angle       1.92909 (    2)
  covalent geometry    : bond        0.00309 ( 7367)
  covalent geometry    : angle       0.50987 ( 9969)

*********************** 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
  126 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 84
  time to evaluate  : 0.758 
Fit side-chains
REVERT: B   44 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8253 (mt0)
REVERT: B  336 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8479 (mt)
REVERT: A  106 MET cc_start: 0.6791 (tpt) cc_final: 0.6335 (tmm)
REVERT: A  175 LEU cc_start: 0.7462 (mt) cc_final: 0.7240 (mt)
REVERT: A  183 ARG cc_start: 0.5180 (ttm-80) cc_final: 0.4688 (ttm170)
REVERT: A  190 VAL cc_start: 0.1719 (OUTLIER) cc_final: 0.1459 (t)
REVERT: A  203 MET cc_start: 0.4233 (ttt) cc_final: 0.3811 (ppp)
REVERT: A  242 LYS cc_start: 0.8136 (tttt) cc_final: 0.7912 (tttm)
REVERT: A  247 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7341 (mtm-85)
REVERT: C   18 MET cc_start: 0.7937 (ttp) cc_final: 0.7542 (tmm)
REVERT: C   24 ARG cc_start: 0.7456 (ptm160) cc_final: 0.7078 (ptp90)
REVERT: C  233 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7489 (p)
REVERT: C  249 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8214 (tt)
REVERT: C  279 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7388 (mtpt)
  outliers start: 42
  outliers final: 20
  residues processed: 118
  average time/residue: 1.2523
  time to fit residues: 155.7218
Evaluate side-chains
  106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
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   59 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  117 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  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:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0000
   chunk 60 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 79 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6184

-------------------------------------------------------------------------------
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 = 0.4130 r_free = 0.4130 target = 0.177112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.133510 restraints weight = 8120.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.18
r_work: 0.3378 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7368  Z= 0.107
  Angle     :  0.485   7.238   9971  Z= 0.258
  Chirality :  0.040   0.159   1149
  Planarity :  0.004   0.049   1255
  Dihedral  :  4.360  42.892   1003
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.32 %
    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:  2.31 (0.28), residues: 386
  sheet:  1.30 (0.39), residues: 161
  loop : -1.92 (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   0.004   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03687 (  348)
  hydrogen bonds       : angle       3.61383 ( 1020)
  SS BOND              : bond        0.00584 (    1)
  SS BOND              : angle       1.49275 (    2)
  covalent geometry    : bond        0.00236 ( 7367)
  covalent geometry    : angle       0.48411 ( 9969)

*********************** 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
  119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8192 (mt0)
REVERT: B  325 MET cc_start: 0.8949 (mmt) cc_final: 0.8560 (mmt)
REVERT: A  106 MET cc_start: 0.6663 (tpt) cc_final: 0.6295 (tmm)
REVERT: A  175 LEU cc_start: 0.7297 (mt) cc_final: 0.6972 (mp)
REVERT: A  183 ARG cc_start: 0.5061 (ttm-80) cc_final: 0.4537 (ttm170)
REVERT: A  190 VAL cc_start: 0.1697 (OUTLIER) cc_final: 0.1436 (t)
REVERT: A  203 MET cc_start: 0.4335 (ttt) cc_final: 0.3811 (ppp)
REVERT: A  242 LYS cc_start: 0.8087 (tttt) cc_final: 0.7856 (tttm)
REVERT: A  333 ARG cc_start: 0.6098 (OUTLIER) cc_final: 0.5072 (tpt170)
REVERT: C   18 MET cc_start: 0.7810 (ttp) cc_final: 0.7415 (tmm)
REVERT: C   24 ARG cc_start: 0.7280 (ptm160) cc_final: 0.6898 (ptp90)
REVERT: C  233 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7465 (p)
REVERT: C  249 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8089 (tt)
REVERT: C  279 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7338 (mtpt)
  outliers start: 37
  outliers final: 20
  residues processed: 112
  average time/residue: 1.1673
  time to fit residues: 138.3861
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
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 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  117 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 TRP
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 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  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 C residue  354 PHE
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:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 59 optimal weight:    0.4980
   chunk 30 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.173934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.129620 restraints weight = 8261.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.24
r_work: 0.3314 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7368  Z= 0.165
  Angle     :  0.538   6.960   9971  Z= 0.285
  Chirality :  0.042   0.164   1149
  Planarity :  0.004   0.041   1255
  Dihedral  :  4.563  41.162   1003
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 23.45 %
    Favored  : 71.61 %
  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:  0.65 (0.28), residues: 908
  helix:  2.18 (0.28), residues: 385
  sheet:  1.13 (0.39), residues: 161
  loop : -1.99 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.006   0.001   HIS A 182 
 PHE   0.015   0.002   PHE C 189 
 TYR   0.013   0.001   TYR A 128 
 ARG   0.004   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04621 (  348)
  hydrogen bonds       : angle       3.81977 ( 1020)
  SS BOND              : bond        0.00788 (    1)
  SS BOND              : angle       1.68475 (    2)
  covalent geometry    : bond        0.00394 ( 7367)
  covalent geometry    : angle       0.53758 ( 9969)

*********************** 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: 39
    poor density    : 80
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: B  336 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8480 (mt)
REVERT: A  106 MET cc_start: 0.6789 (tpt) cc_final: 0.6369 (tmm)
REVERT: A  175 LEU cc_start: 0.7451 (mt) cc_final: 0.7101 (mp)
REVERT: A  183 ARG cc_start: 0.5237 (ttm-80) cc_final: 0.4738 (ttm170)
REVERT: A  190 VAL cc_start: 0.1584 (OUTLIER) cc_final: 0.1339 (t)
REVERT: A  203 MET cc_start: 0.4390 (ttt) cc_final: 0.3659 (ppp)
REVERT: A  242 LYS cc_start: 0.8143 (tttt) cc_final: 0.7917 (tttm)
REVERT: A  247 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7389 (mtm-85)
REVERT: A  333 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5091 (tpt170)
REVERT: C   18 MET cc_start: 0.7978 (ttp) cc_final: 0.7587 (tmm)
REVERT: C   24 ARG cc_start: 0.7544 (ptm160) cc_final: 0.7148 (ptp90)
REVERT: C  233 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7511 (p)
REVERT: C  249 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8212 (tt)
REVERT: C  279 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7405 (mtpt)
  outliers start: 39
  outliers final: 22
  residues processed: 111
  average time/residue: 1.2415
  time to fit residues: 145.2349
Evaluate side-chains
  108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
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  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  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  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  279 LYS
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:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0980
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4119 r_free = 0.4119 target = 0.176248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132228 restraints weight = 8241.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.24
r_work: 0.3350 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7368  Z= 0.113
  Angle     :  0.484   7.024   9971  Z= 0.258
  Chirality :  0.040   0.157   1149
  Planarity :  0.003   0.040   1255
  Dihedral  :  4.328  41.877   1003
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.21 %
    Favored  : 71.61 %
  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:  2.33 (0.28), residues: 385
  sheet:  1.21 (0.39), residues: 166
  loop : -1.98 (0.27), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 182 
 PHE   0.013   0.001   PHE C 189 
 TYR   0.010   0.001   TYR A 128 
 ARG   0.003   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03797 (  348)
  hydrogen bonds       : angle       3.64052 ( 1020)
  SS BOND              : bond        0.00669 (    1)
  SS BOND              : angle       1.65768 (    2)
  covalent geometry    : bond        0.00254 ( 7367)
  covalent geometry    : angle       0.48388 ( 9969)

*********************** 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
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: B  325 MET cc_start: 0.8986 (mmt) cc_final: 0.8619 (mmt)
REVERT: B  336 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8507 (mt)
REVERT: A  106 MET cc_start: 0.6750 (tpt) cc_final: 0.6343 (tmm)
REVERT: A  175 LEU cc_start: 0.7421 (mt) cc_final: 0.7089 (mp)
REVERT: A  183 ARG cc_start: 0.5172 (ttm-80) cc_final: 0.4712 (ttm170)
REVERT: A  190 VAL cc_start: 0.1629 (OUTLIER) cc_final: 0.1331 (t)
REVERT: A  203 MET cc_start: 0.4224 (ttt) cc_final: 0.3585 (ppp)
REVERT: A  242 LYS cc_start: 0.8139 (tttt) cc_final: 0.7784 (tttp)
REVERT: A  333 ARG cc_start: 0.6045 (OUTLIER) cc_final: 0.5068 (tpt170)
REVERT: C   18 MET cc_start: 0.7930 (ttp) cc_final: 0.7554 (tmm)
REVERT: C   24 ARG cc_start: 0.7426 (ptm160) cc_final: 0.7057 (ptp90)
REVERT: C  233 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7480 (p)
REVERT: C  249 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8191 (tt)
REVERT: C  279 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7442 (mtpt)
  outliers start: 33
  outliers final: 20
  residues processed: 106
  average time/residue: 1.3403
  time to fit residues: 150.0312
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  : 0.707 
-------------------------------------------------------------------------------
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 B residue  336 LEU
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  117 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  279 LYS
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 63 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   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:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.4092 r_free = 0.4092 target = 0.173720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.129431 restraints weight = 8326.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.28
r_work: 0.3306 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7368  Z= 0.170
  Angle     :  0.548   7.004   9971  Z= 0.288
  Chirality :  0.042   0.164   1149
  Planarity :  0.004   0.041   1255
  Dihedral  :  4.533  40.863   1003
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 24.71 %
    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:  0.62 (0.28), residues: 908
  helix:  2.14 (0.28), residues: 385
  sheet:  1.20 (0.39), residues: 160
  loop : -2.02 (0.27), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 182 
 PHE   0.015   0.002   PHE C 189 
 TYR   0.013   0.001   TYR A 128 
 ARG   0.003   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04623 (  348)
  hydrogen bonds       : angle       3.83520 ( 1020)
  SS BOND              : bond        0.00788 (    1)
  SS BOND              : angle       1.61904 (    2)
  covalent geometry    : bond        0.00408 ( 7367)
  covalent geometry    : angle       0.54759 ( 9969)

********************** 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
  106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 78
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: B  336 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8469 (mt)
REVERT: A  106 MET cc_start: 0.6744 (tpt) cc_final: 0.6342 (tmm)
REVERT: A  175 LEU cc_start: 0.7429 (mt) cc_final: 0.7087 (mp)
REVERT: A  183 ARG cc_start: 0.5199 (ttm-80) cc_final: 0.4730 (ttm170)
REVERT: A  190 VAL cc_start: 0.1419 (OUTLIER) cc_final: 0.1129 (t)
REVERT: A  203 MET cc_start: 0.4213 (ttt) cc_final: 0.3554 (ppp)
REVERT: A  242 LYS cc_start: 0.8162 (tttt) cc_final: 0.7813 (tttp)
REVERT: A  333 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.5095 (tpt170)
REVERT: C   18 MET cc_start: 0.7966 (ttp) cc_final: 0.7567 (tmm)
REVERT: C   24 ARG cc_start: 0.7545 (ptm160) cc_final: 0.7143 (ptp90)
REVERT: C  233 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7519 (p)
REVERT: C  249 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8149 (tt)
REVERT: C  279 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7425 (mtpt)
  outliers start: 28
  outliers final: 21
  residues processed: 102
  average time/residue: 1.2026
  time to fit residues: 129.8984
Evaluate side-chains
  103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
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 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  117 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  279 LYS
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:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 17 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 = 0.174603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.130364 restraints weight = 8238.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.22
r_work: 0.3328 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7368  Z= 0.144
  Angle     :  0.527   8.276   9971  Z= 0.278
  Chirality :  0.041   0.162   1149
  Planarity :  0.004   0.040   1255
  Dihedral  :  4.472  41.536   1003
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.10 %
    Favored  : 71.61 %
  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:  0.64 (0.28), residues: 908
  helix:  2.17 (0.28), residues: 385
  sheet:  1.21 (0.39), residues: 161
  loop : -2.03 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 210 
 PHE   0.014   0.001   PHE C 189 
 TYR   0.012   0.001   TYR A 128 
 ARG   0.003   0.000   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04296 (  348)
  hydrogen bonds       : angle       3.77542 ( 1020)
  SS BOND              : bond        0.00726 (    1)
  SS BOND              : angle       1.62613 (    2)
  covalent geometry    : bond        0.00339 ( 7367)
  covalent geometry    : angle       0.52671 ( 9969)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5723.84 seconds
wall clock time: 99 minutes 27.36 seconds (5967.36 seconds total)