Starting phenix.real_space_refine
on Thu Sep 18 01:22:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8z9a_39858/09_2025/8z9a_39858_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8z9a_39858/09_2025/8z9a_39858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8z9a_39858/09_2025/8z9a_39858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8z9a_39858/09_2025/8z9a_39858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8z9a_39858/09_2025/8z9a_39858_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8z9a_39858/09_2025/8z9a_39858_neut.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   0.129
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      72      5.16       5
     C    8695      2.51       5
     N    1981      2.21       5
     O    2266      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13021
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3292
          Classifications: {'peptide': 406}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 395}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 406, 3292
          Classifications: {'peptide': 406}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 395}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3140
          Classifications: {'peptide': 388}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 379}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2905
          Classifications: {'peptide': 357}
          Link IDs: {'PTRANS': 7, 'TRANS': 349}
    Chain: "A"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 108
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 162
          Unusual residues: {'PC1': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 54
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 68
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 68
          Unusual residues: {'PC1': 1, 'SOU': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.11, per 1000 atoms: 0.24
  Number of scatterers: 13021
  At special positions: 0
  Unit cell: (115.56, 129.47, 132.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     P       7     15.00
     O    2266      8.00
     N    1981      7.00
     C    8695      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 581.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2994

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 4 sheets defined
      80.7% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 12
      removed outlier: 3.593A  pdb=" N   ASP A  11 " --> pdb=" O   GLY A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 23
      removed outlier: 3.657A  pdb=" N   GLY A  23 " --> pdb=" O   ILE A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 65
      removed outlier: 3.740A  pdb=" N   MET A  63 " --> pdb=" O   ILE A  59 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 95
      removed outlier: 3.754A  pdb=" N   HIS A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   SER A  86 " --> pdb=" O   PHE A  82 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL A  91 " --> pdb=" O   MET A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 105
      removed outlier: 3.933A  pdb=" N   PHE A 100 " --> pdb=" O   GLY A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 116 through 152
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 191 through 237
      removed outlier: 3.525A  pdb=" N   GLU A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 245
      removed outlier: 3.700A  pdb=" N   SER A 245 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 336
    Processing helix  chain 'A' and resid 337 through 359
      removed outlier: 3.787A  pdb=" N   VAL A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 405
      removed outlier: 3.558A  pdb=" N   ILE A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   PHE A 385 " --> pdb=" O   GLN A 381 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   HIS A 388 " --> pdb=" O   MET A 384 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL A 399 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   MET A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   GLU A 401 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 426
    Processing helix  chain 'A' and resid 441 through 463
      removed outlier: 3.549A  pdb=" N   PHE A 445 " --> pdb=" O   SER A 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 12
      removed outlier: 3.521A  pdb=" N   ASP B  11 " --> pdb=" O   GLY B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 22
    Processing helix  chain 'B' and resid 36 through 66
    Processing helix  chain 'B' and resid 69 through 95
      removed outlier: 3.807A  pdb=" N   HIS B  85 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   SER B  86 " --> pdb=" O   PHE B  82 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   THR B  95 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 105
      removed outlier: 3.888A  pdb=" N   PHE B 100 " --> pdb=" O   GLY B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 115
      No H-bonds generated for 'chain 'B' and resid 113 through 115'
    Processing helix  chain 'B' and resid 116 through 152
      removed outlier: 3.656A  pdb=" N   SER B 121 " --> pdb=" O   ALA B 117 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LYS B 126 " --> pdb=" O   ARG B 122 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN B 133 " --> pdb=" O   SER B 129 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE B 143 " --> pdb=" O   SER B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 156
      removed outlier: 4.256A  pdb=" N   GLY B 156 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 153 through 156'
    Processing helix  chain 'B' and resid 191 through 237
      removed outlier: 3.522A  pdb=" N   TYR B 195 " --> pdb=" O   HIS B 191 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   MET B 216 " --> pdb=" O   HIS B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 245
      removed outlier: 3.590A  pdb=" N   SER B 245 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 336
    Processing helix  chain 'B' and resid 337 through 359
      removed outlier: 3.834A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   THR B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 398
      removed outlier: 3.961A  pdb=" N   PHE B 385 " --> pdb=" O   GLN B 381 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   HIS B 388 " --> pdb=" O   MET B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 405
    Processing helix  chain 'B' and resid 412 through 426
    Processing helix  chain 'B' and resid 441 through 463
      removed outlier: 3.672A  pdb=" N   PHE B 445 " --> pdb=" O   SER B 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 12
    Processing helix  chain 'C' and resid 12 through 22
    Processing helix  chain 'C' and resid 36 through 66
    Processing helix  chain 'C' and resid 69 through 95
      removed outlier: 3.698A  pdb=" N   HIS C  85 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   SER C  86 " --> pdb=" O   PHE C  82 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL C  91 " --> pdb=" O   MET C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 107
      removed outlier: 3.906A  pdb=" N   PHE C 100 " --> pdb=" O   GLY C  96 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   TRP C 107 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 149
      removed outlier: 4.176A  pdb=" N   LYS C 126 " --> pdb=" O   ARG C 122 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   SER C 127 " --> pdb=" O   PHE C 123 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LEU C 135 " --> pdb=" O   MET C 131 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ILE C 143 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 237
      removed outlier: 3.702A  pdb=" N   ILE C 196 " --> pdb=" O   GLY C 192 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   GLU C 217 " --> pdb=" O   SER C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 237 through 246
    Processing helix  chain 'C' and resid 304 through 336
    Processing helix  chain 'C' and resid 336 through 358
      removed outlier: 3.838A  pdb=" N   LEU C 340 " --> pdb=" O   TYR C 336 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL C 349 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 397
      removed outlier: 3.903A  pdb=" N   ILE C 382 " --> pdb=" O   SER C 378 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   PHE C 385 " --> pdb=" O   GLN C 381 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   HIS C 388 " --> pdb=" O   MET C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 398 through 406
    Processing helix  chain 'C' and resid 407 through 411
    Processing helix  chain 'C' and resid 412 through 426
    Processing helix  chain 'C' and resid 441 through 463
    Processing helix  chain 'D' and resid 5 through 14
      removed outlier: 3.954A  pdb=" N   MET D   9 " --> pdb=" O   ASP D   5 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 20 through 46
    Processing helix  chain 'D' and resid 50 through 77
      removed outlier: 3.566A  pdb=" N   PHE D  56 " --> pdb=" O   THR D  52 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS D  77 " --> pdb=" O   PHE D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 89
    Processing helix  chain 'D' and resid 94 through 124
      Proline residue:  D 119  - end of helix
    Processing helix  chain 'D' and resid 149 through 200
      removed outlier: 3.925A  pdb=" N   SER D 163 " --> pdb=" O   VAL D 159 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL D 164 " --> pdb=" O   TYR D 160 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE D 174 " --> pdb=" O   GLU D 170 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   PHE D 178 " --> pdb=" O   ILE D 174 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ILE D 179 " --> pdb=" O   ASN D 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 256
      removed outlier: 5.032A  pdb=" N   LYS D 231 " --> pdb=" O   ILE D 227 " (cutoff:3.500A)
      Proline residue:  D 232  - end of helix
    Processing helix  chain 'D' and resid 260 through 262
      No H-bonds generated for 'chain 'D' and resid 260 through 262'
    Processing helix  chain 'D' and resid 263 through 271
      removed outlier: 3.952A  pdb=" N   ALA D 269 " --> pdb=" O   SER D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 287
      removed outlier: 3.746A  pdb=" N   ASN D 277 " --> pdb=" O   ALA D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 290 through 300
      removed outlier: 3.876A  pdb=" N   LYS D 294 " --> pdb=" O   ASP D 290 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ILE D 295 " --> pdb=" O   LEU D 291 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE D 300 " --> pdb=" O   LEU D 296 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 301 through 306
    Processing helix  chain 'D' and resid 310 through 322
    Processing helix  chain 'D' and resid 337 through 360
      removed outlier: 3.930A  pdb=" N   LEU D 345 " --> pdb=" O   LEU D 341 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   LYS D 346 " --> pdb=" O   LEU D 342 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   MET D 347 " --> pdb=" O   LYS D 343 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 163
    Processing sheet with id=AA2, first strand: chain 'A' and resid 433 through 434
      removed outlier: 3.919A  pdb=" N   PHE A 438 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 163
    Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 330

    960 hydrogen bonds defined for protein.
    2862 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: 1.97

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1889
        1.31 -     1.44: 3948
        1.44 -     1.57: 7391
        1.57 -     1.69: 15
        1.69 -     1.82: 116
  Bond restraints: 13359
  Sorted by residual:
  bond pdb=" CA  SER D 271 "
       pdb=" CB  SER D 271 "
    ideal  model  delta    sigma   weight residual
    1.536  1.443  0.093 1.53e-02 4.27e+03 3.72e+01
  bond pdb=" CA  SER D 270 "
       pdb=" CB  SER D 270 "
    ideal  model  delta    sigma   weight residual
    1.531  1.438  0.093 1.72e-02 3.38e+03 2.90e+01
  bond pdb=" C21 PC1 B 502 "
       pdb=" O21 PC1 B 502 "
    ideal  model  delta    sigma   weight residual
    1.331  1.406 -0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" C21 PC1 C 501 "
       pdb=" O21 PC1 C 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.405 -0.074 2.00e-02 2.50e+03 1.37e+01
  bond pdb=" C21 PC1 A 502 "
       pdb=" O21 PC1 A 502 "
    ideal  model  delta    sigma   weight residual
    1.331  1.405 -0.074 2.00e-02 2.50e+03 1.35e+01
  ... (remaining 13354 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.92: 17702
        2.92 -     5.84: 340
        5.84 -     8.77: 30
        8.77 -    11.69: 4
       11.69 -    14.61: 8
  Bond angle restraints: 18084
  Sorted by residual:
  angle pdb=" CA  PRO D 119 "
        pdb=" N   PRO D 119 "
        pdb=" CD  PRO D 119 "
      ideal   model   delta    sigma   weight residual
     112.00  103.08    8.92 1.40e+00 5.10e-01 4.06e+01
  angle pdb=" N   ILE D 124 "
        pdb=" CA  ILE D 124 "
        pdb=" C   ILE D 124 "
      ideal   model   delta    sigma   weight residual
     112.29  106.85    5.44 9.40e-01 1.13e+00 3.35e+01
  angle pdb=" N   SER D 271 "
        pdb=" CA  SER D 271 "
        pdb=" C   SER D 271 "
      ideal   model   delta    sigma   weight residual
     113.72  106.48    7.24 1.30e+00 5.92e-01 3.10e+01
  angle pdb=" O12 PC1 C 501 "
        pdb=" P   PC1 C 501 "
        pdb=" O14 PC1 C 501 "
      ideal   model   delta    sigma   weight residual
     123.67  109.06   14.61 3.00e+00 1.11e-01 2.37e+01
  angle pdb=" O12 PC1 B 502 "
        pdb=" P   PC1 B 502 "
        pdb=" O14 PC1 B 502 "
      ideal   model   delta    sigma   weight residual
     123.67  109.29   14.38 3.00e+00 1.11e-01 2.30e+01
  ... (remaining 18079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 6812
       17.71 -    35.42: 731
       35.42 -    53.14: 212
       53.14 -    70.85: 60
       70.85 -    88.56: 11
  Dihedral angle restraints: 7826
    sinusoidal: 3199
      harmonic: 4627
  Sorted by residual:
  dihedral pdb=" CA  ASP D 133 "
           pdb=" C   ASP D 133 "
           pdb=" N   PRO D 134 "
           pdb=" CA  PRO D 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.40  -45.60     0      5.00e+00 4.00e-02 8.32e+01
  dihedral pdb=" CA  VAL D 307 "
           pdb=" C   VAL D 307 "
           pdb=" N   SER D 308 "
           pdb=" CA  SER D 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.93  -23.07     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  SER D 310 "
           pdb=" C   SER D 310 "
           pdb=" N   PHE D 311 "
           pdb=" CA  PHE D 311 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.14   19.86     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 7823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1357
       0.032 -    0.064: 505
       0.064 -    0.096: 151
       0.096 -    0.127: 42
       0.127 -    0.159: 8
  Chirality restraints: 2063
  Sorted by residual:
  chirality pdb=" C2  PC1 B 502 "
            pdb=" C1  PC1 B 502 "
            pdb=" C3  PC1 B 502 "
            pdb=" O21 PC1 B 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.16 2.00e-01 2.50e+01 6.34e-01
  chirality pdb=" CB  ILE C 237 "
            pdb=" CA  ILE C 237 "
            pdb=" CG1 ILE C 237 "
            pdb=" CG2 ILE C 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.14e-01
  chirality pdb=" C2  PC1 A 502 "
            pdb=" C1  PC1 A 502 "
            pdb=" C3  PC1 A 502 "
            pdb=" O21 PC1 A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.33   -0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 2060 not shown)

  Planarity restraints: 2140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 SOU D 402 "    0.051 2.00e-02 2.50e+03   1.38e-01 2.39e+02
        pdb=" C11 SOU D 402 "    0.015 2.00e-02 2.50e+03
        pdb=" C12 SOU D 402 "   -0.124 2.00e-02 2.50e+03
        pdb=" C8  SOU D 402 "   -0.165 2.00e-02 2.50e+03
        pdb=" C9  SOU D 402 "    0.224 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3  SOU D 402 "   -0.106 2.00e-02 2.50e+03   8.76e-02 9.59e+01
        pdb=" C4  SOU D 402 "    0.137 2.00e-02 2.50e+03
        pdb=" C5  SOU D 402 "    0.032 2.00e-02 2.50e+03
        pdb=" C6  SOU D 402 "    0.019 2.00e-02 2.50e+03
        pdb=" C7  SOU D 402 "   -0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 118 "   -0.085 5.00e-02 4.00e+02   1.23e-01 2.43e+01
        pdb=" N   PRO D 119 "    0.213 5.00e-02 4.00e+02
        pdb=" CA  PRO D 119 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO D 119 "   -0.066 5.00e-02 4.00e+02
  ... (remaining 2137 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 340
        2.71 -     3.26: 13266
        3.26 -     3.81: 21982
        3.81 -     4.35: 26751
        4.35 -     4.90: 46142
  Nonbonded interactions: 108481
  Sorted by model distance:
  nonbonded pdb=" O   VAL D 116 "
            pdb=" OH  TYR D 157 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OE2 GLU A 320 "
            pdb=" OH  TYR C 409 "
     model   vdw
     2.180 3.040
  nonbonded pdb=" O   PHE D  10 "
            pdb=" OG1 THR D  14 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OH  TYR B 409 "
            pdb=" OE2 GLU C 320 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OH  TYR C  92 "
            pdb=" OG  SER C 338 "
     model   vdw
     2.215 3.040
  ... (remaining 108476 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 156 or resid 175 through 501))
  selection = (chain 'B' and (resid 5 through 156 or resid 175 through 501))
  selection = chain 'C'
}

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:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.340
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  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:6.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
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      :  0.005   0.093  13359  Z= 0.245
  Angle     :  0.835  14.611  18084  Z= 0.361
  Chirality :  0.039   0.159   2063
  Planarity :  0.006   0.138   2140
  Dihedral  : 16.754  88.562   4832
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.41 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.22), residues: 1541
  helix:  2.10 (0.15), residues: 1209
  sheet:  1.55 (1.04), residues: 24
  loop : -1.28 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 102 
 TYR   0.021   0.001   TYR C  44 
 PHE   0.020   0.001   PHE B 385 
 TRP   0.009   0.001   TRP B  13 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (13359)
  covalent geometry    : angle       0.83510 (18084)
  hydrogen bonds       : bond        0.12246 (  960)
  hydrogen bonds       : angle       4.88103 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: D    5 ASP cc_start: 0.7007 (t0) cc_final: 0.6762 (t0)
  outliers start: 22
  outliers final: 19
  residues processed: 188
  average time/residue: 0.5121
  time to fit residues: 106.3110
Evaluate side-chains
  175 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain B residue  129 SER
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  447 SER
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain C residue   15 ASN
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  397 SER
Chi-restraints excluded: chain C residue  443 ASP
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  275 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
A 322 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 ASN
C  72 GLN
C 214 ASN
** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.148744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.102942 restraints weight = 15292.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.09
r_work: 0.2935 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.0848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13359  Z= 0.204
  Angle     :  0.516   7.738  18084  Z= 0.271
  Chirality :  0.040   0.161   2063
  Planarity :  0.004   0.077   2140
  Dihedral  : 12.034  83.764   2040
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.15 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.22), residues: 1541
  helix:  2.32 (0.14), residues: 1217
  sheet:  1.61 (1.06), residues: 24
  loop : -1.29 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 102 
 TYR   0.019   0.001   TYR C  53 
 PHE   0.027   0.001   PHE B 385 
 TRP   0.011   0.001   TRP B 408 
 HIS   0.005   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (13359)
  covalent geometry    : angle       0.51553 (18084)
  hydrogen bonds       : bond        0.05098 (  960)
  hydrogen bonds       : angle       3.60373 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 168
  time to evaluate  : 0.559 
Fit side-chains
REVERT: A  312 ARG cc_start: 0.8333 (ttt180) cc_final: 0.8017 (mtp180)
REVERT: A  384 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8112 (ttp)
REVERT: B   42 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7065 (mmtt)
REVERT: B  178 ARG cc_start: 0.8562 (ttm170) cc_final: 0.8289 (ttm170)
REVERT: C  136 ILE cc_start: 0.6403 (OUTLIER) cc_final: 0.6187 (mm)
REVERT: C  178 ARG cc_start: 0.6441 (ttm-80) cc_final: 0.5801 (ttt180)
REVERT: D    5 ASP cc_start: 0.6880 (t0) cc_final: 0.6546 (t0)
REVERT: D  309 LYS cc_start: 0.8917 (tmtt) cc_final: 0.8711 (tptp)
  outliers start: 56
  outliers final: 24
  residues processed: 199
  average time/residue: 0.5234
  time to fit residues: 114.8467
Evaluate side-chains
  179 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  376 MET
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  201 LEU
Chi-restraints excluded: chain C residue  228 CYS
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain D residue   26 THR
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  247 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 42 optimal weight:    0.0370
   chunk 58 optimal weight:    0.0060
   chunk 5 optimal weight:    0.6980
   chunk 127 optimal weight:    0.6980
   chunk 121 optimal weight:    2.9990
   chunk 137 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 89 optimal weight:    6.9990
   chunk 129 optimal weight:    2.9990
   chunk 149 optimal weight:    0.8980
   chunk 148 optimal weight:    2.9990
   overall best weight:    0.4674

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 240 ASN ** 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 = 0.3795 r_free = 0.3795 target = 0.154496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.108557 restraints weight = 15364.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.14
r_work: 0.3063 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2912 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13359  Z= 0.102
  Angle     :  0.418   7.645  18084  Z= 0.222
  Chirality :  0.036   0.158   2063
  Planarity :  0.003   0.066   2140
  Dihedral  : 11.100  76.772   2022
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.07 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.07 (0.22), residues: 1541
  helix:  2.76 (0.14), residues: 1217
  sheet:  1.64 (1.04), residues: 24
  loop : -1.19 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 178 
 TYR   0.015   0.001   TYR C  53 
 PHE   0.016   0.001   PHE A 385 
 TRP   0.007   0.001   TRP B  13 
 HIS   0.003   0.001   HIS C 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 (13359)
  covalent geometry    : angle       0.41823 (18084)
  hydrogen bonds       : bond        0.04004 (  960)
  hydrogen bonds       : angle       3.28004 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 177
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  178 ARG cc_start: 0.8892 (ttm-80) cc_final: 0.8662 (ttm-80)
REVERT: A  312 ARG cc_start: 0.8286 (ttt180) cc_final: 0.7973 (mtp180)
REVERT: B   42 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7125 (mmtt)
REVERT: B  178 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8210 (ttm170)
REVERT: C  178 ARG cc_start: 0.6608 (ttm-80) cc_final: 0.6172 (ttt180)
REVERT: D    5 ASP cc_start: 0.6873 (t0) cc_final: 0.6512 (t0)
  outliers start: 34
  outliers final: 10
  residues processed: 195
  average time/residue: 0.5032
  time to fit residues: 108.1476
Evaluate side-chains
  168 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 158
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   89 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   chunk 125 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0170
   chunk 49 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.5422

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 HIS
C 424 GLN
D 214 GLN
** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 253 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.103991 restraints weight = 15329.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 2.09
r_work: 0.2878 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2724 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  13359  Z= 0.165
  Angle     :  0.477   8.542  18084  Z= 0.249
  Chirality :  0.038   0.158   2063
  Planarity :  0.003   0.062   2140
  Dihedral  : 11.138  85.967   2019
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.14 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.98 (0.22), residues: 1541
  helix:  2.68 (0.14), residues: 1217
  sheet:  1.65 (1.01), residues: 24
  loop : -1.16 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 102 
 TYR   0.022   0.001   TYR C  53 
 PHE   0.023   0.001   PHE B 385 
 TRP   0.009   0.001   TRP B  13 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (13359)
  covalent geometry    : angle       0.47713 (18084)
  hydrogen bonds       : bond        0.04614 (  960)
  hydrogen bonds       : angle       3.37399 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 168
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  178 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8450 (ttm-80)
REVERT: A  312 ARG cc_start: 0.8047 (ttt180) cc_final: 0.7706 (mtp180)
REVERT: A  395 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7921 (tt0)
REVERT: B   42 LYS cc_start: 0.7337 (mtpt) cc_final: 0.6818 (mmtt)
REVERT: B  178 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7773 (ttm170)
REVERT: C  178 ARG cc_start: 0.6639 (ttm-80) cc_final: 0.6142 (ttt90)
REVERT: C  216 MET cc_start: 0.7681 (mmp) cc_final: 0.7387 (mmt)
REVERT: C  310 LEU cc_start: 0.7279 (mt) cc_final: 0.7058 (tp)
REVERT: C  401 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7519 (mm-30)
REVERT: D    5 ASP cc_start: 0.6861 (t0) cc_final: 0.6498 (t0)
REVERT: D  309 LYS cc_start: 0.8642 (tmtt) cc_final: 0.8157 (tptt)
  outliers start: 52
  outliers final: 23
  residues processed: 205
  average time/residue: 0.5054
  time to fit residues: 114.5438
Evaluate side-chains
  184 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  407 HIS
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  275 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 141 optimal weight:    0.9980
   chunk 144 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 146 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 50 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 104 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 HIS
** D 240 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 = 0.3774 r_free = 0.3774 target = 0.152298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.106553 restraints weight = 15306.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 2.10
r_work: 0.2912 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13359  Z= 0.117
  Angle     :  0.442   9.029  18084  Z= 0.231
  Chirality :  0.036   0.152   2063
  Planarity :  0.003   0.060   2140
  Dihedral  : 10.838  86.149   2019
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.76 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.25 (0.22), residues: 1541
  helix:  2.85 (0.14), residues: 1213
  sheet:  1.75 (0.99), residues: 24
  loop : -0.94 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 102 
 TYR   0.018   0.001   TYR C  53 
 PHE   0.017   0.001   PHE A 385 
 TRP   0.008   0.001   TRP B  13 
 HIS   0.018   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (13359)
  covalent geometry    : angle       0.44167 (18084)
  hydrogen bonds       : bond        0.04148 (  960)
  hydrogen bonds       : angle       3.26947 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 0.436 
Fit side-chains
REVERT: A  178 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8467 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7715 (mp0)
REVERT: A  312 ARG cc_start: 0.8029 (ttt180) cc_final: 0.7684 (mtp180)
REVERT: A  395 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7862 (tt0)
REVERT: B   42 LYS cc_start: 0.7356 (mtpt) cc_final: 0.6867 (mmtt)
REVERT: B  178 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7952 (ttm170)
REVERT: B  199 PHE cc_start: 0.8355 (t80) cc_final: 0.7947 (t80)
REVERT: B  462 LEU cc_start: 0.7202 (tt) cc_final: 0.6861 (mp)
REVERT: C  178 ARG cc_start: 0.6928 (ttm-80) cc_final: 0.6513 (ttt180)
REVERT: C  401 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7404 (mm-30)
REVERT: D    5 ASP cc_start: 0.6820 (t0) cc_final: 0.6520 (t0)
REVERT: D   86 GLN cc_start: 0.7938 (tp-100) cc_final: 0.7725 (tp-100)
  outliers start: 36
  outliers final: 17
  residues processed: 194
  average time/residue: 0.5172
  time to fit residues: 110.2874
Evaluate side-chains
  179 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain C residue   22 SER
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   66 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 150 optimal weight:    0.1980
   chunk 63 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 151 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 98 optimal weight:    8.9990
   chunk 84 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 HIS
** D 240 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 = 0.3763 r_free = 0.3763 target = 0.151379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.105200 restraints weight = 15191.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.10
r_work: 0.2926 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13359  Z= 0.136
  Angle     :  0.460   9.995  18084  Z= 0.240
  Chirality :  0.037   0.152   2063
  Planarity :  0.003   0.059   2140
  Dihedral  : 10.809  87.572   2019
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 17.83 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.19 (0.22), residues: 1541
  helix:  2.82 (0.14), residues: 1214
  sheet:  1.78 (0.99), residues: 24
  loop : -1.00 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 102 
 TYR   0.023   0.001   TYR B  92 
 PHE   0.020   0.001   PHE B 385 
 TRP   0.009   0.001   TRP B  13 
 HIS   0.003   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (13359)
  covalent geometry    : angle       0.45976 (18084)
  hydrogen bonds       : bond        0.04320 (  960)
  hydrogen bonds       : angle       3.30180 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 168
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 ARG cc_start: 0.8865 (ttm-80) cc_final: 0.8555 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7753 (mp0)
REVERT: A  312 ARG cc_start: 0.8156 (ttt180) cc_final: 0.7793 (mtp180)
REVERT: A  395 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7997 (tt0)
REVERT: B   42 LYS cc_start: 0.7499 (mtpt) cc_final: 0.6964 (mmtt)
REVERT: B  178 ARG cc_start: 0.8337 (ttm170) cc_final: 0.8079 (ttm170)
REVERT: B  199 PHE cc_start: 0.8494 (t80) cc_final: 0.8093 (t80)
REVERT: B  462 LEU cc_start: 0.7333 (tt) cc_final: 0.6979 (mp)
REVERT: C  178 ARG cc_start: 0.6994 (ttm-80) cc_final: 0.6633 (ttt90)
REVERT: D    5 ASP cc_start: 0.6871 (t0) cc_final: 0.6551 (t0)
  outliers start: 39
  outliers final: 23
  residues processed: 198
  average time/residue: 0.5352
  time to fit residues: 116.7416
Evaluate side-chains
  186 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain C residue   22 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  275 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 151 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 143 optimal weight:    8.9990
   chunk 57 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 HIS
** D 240 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 = 0.3766 r_free = 0.3766 target = 0.151665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.105620 restraints weight = 15284.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.12
r_work: 0.2931 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13359  Z= 0.130
  Angle     :  0.454  10.773  18084  Z= 0.236
  Chirality :  0.037   0.146   2063
  Planarity :  0.003   0.057   2140
  Dihedral  : 10.760  88.004   2019
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 17.48 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.23 (0.22), residues: 1541
  helix:  2.84 (0.14), residues: 1214
  sheet:  1.81 (0.98), residues: 24
  loop : -0.98 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 102 
 TYR   0.021   0.001   TYR D 160 
 PHE   0.018   0.001   PHE B 385 
 TRP   0.009   0.001   TRP B  13 
 HIS   0.004   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (13359)
  covalent geometry    : angle       0.45413 (18084)
  hydrogen bonds       : bond        0.04247 (  960)
  hydrogen bonds       : angle       3.27895 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 172
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A  178 ARG cc_start: 0.8831 (ttm-80) cc_final: 0.8525 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7750 (mp0)
REVERT: A  312 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7775 (mtp180)
REVERT: A  384 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8101 (tpp)
REVERT: A  395 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7950 (tt0)
REVERT: B   42 LYS cc_start: 0.7483 (mtpt) cc_final: 0.6983 (mmtt)
REVERT: B  178 ARG cc_start: 0.8304 (ttm170) cc_final: 0.8051 (ttm170)
REVERT: B  199 PHE cc_start: 0.8474 (t80) cc_final: 0.8078 (t80)
REVERT: B  462 LEU cc_start: 0.7304 (tt) cc_final: 0.6995 (mp)
REVERT: C  126 LYS cc_start: 0.5532 (tppt) cc_final: 0.5244 (tppt)
REVERT: C  129 SER cc_start: 0.6776 (t) cc_final: 0.6433 (m)
REVERT: C  178 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6715 (ttt180)
REVERT: C  401 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7628 (mm-30)
REVERT: D    5 ASP cc_start: 0.6845 (t0) cc_final: 0.6566 (t0)
  outliers start: 49
  outliers final: 28
  residues processed: 208
  average time/residue: 0.5018
  time to fit residues: 114.8784
Evaluate side-chains
  195 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  407 HIS
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain C residue   22 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   71 ASP
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  275 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 143 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 26 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0050
   chunk 68 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.0996

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 HIS
** D 240 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 = 0.3766 r_free = 0.3766 target = 0.151643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.105417 restraints weight = 15137.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.11
r_work: 0.2930 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13359  Z= 0.134
  Angle     :  0.467  11.408  18084  Z= 0.241
  Chirality :  0.037   0.137   2063
  Planarity :  0.003   0.056   2140
  Dihedral  : 10.721  88.632   2019
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.98 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.24 (0.22), residues: 1541
  helix:  2.85 (0.14), residues: 1213
  sheet:  1.77 (0.97), residues: 24
  loop : -0.94 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 102 
 TYR   0.024   0.001   TYR B  92 
 PHE   0.019   0.001   PHE B 385 
 TRP   0.010   0.001   TRP B 408 
 HIS   0.006   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (13359)
  covalent geometry    : angle       0.46654 (18084)
  hydrogen bonds       : bond        0.04273 (  960)
  hydrogen bonds       : angle       3.28087 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 167
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 LYS cc_start: 0.7838 (mptm) cc_final: 0.7300 (mmtt)
REVERT: A  178 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8456 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7679 (mp0)
REVERT: A  312 ARG cc_start: 0.8092 (ttt180) cc_final: 0.7745 (mtp180)
REVERT: A  384 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8047 (tpp)
REVERT: A  395 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7903 (tt0)
REVERT: B  178 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7975 (ttm170)
REVERT: B  199 PHE cc_start: 0.8417 (t80) cc_final: 0.8021 (t80)
REVERT: B  461 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6274 (tp40)
REVERT: B  462 LEU cc_start: 0.7238 (tt) cc_final: 0.6953 (mp)
REVERT: C  129 SER cc_start: 0.6729 (t) cc_final: 0.6406 (m)
REVERT: C  178 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6786 (ttm-80)
REVERT: C  216 MET cc_start: 0.7743 (mmp) cc_final: 0.7476 (mmt)
REVERT: D    5 ASP cc_start: 0.6847 (t0) cc_final: 0.6541 (t0)
  outliers start: 45
  outliers final: 27
  residues processed: 199
  average time/residue: 0.5103
  time to fit residues: 111.8706
Evaluate side-chains
  197 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 166
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain C residue   22 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  275 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 125 optimal weight:    2.9990
   chunk 86 optimal weight:    8.9990
   chunk 140 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 407 HIS
** D 240 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 = 0.3763 r_free = 0.3763 target = 0.151366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.105177 restraints weight = 15291.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.12
r_work: 0.2929 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  13359  Z= 0.136
  Angle     :  0.476  12.043  18084  Z= 0.245
  Chirality :  0.037   0.135   2063
  Planarity :  0.003   0.056   2140
  Dihedral  : 10.472  89.490   2019
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.68 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.18 (0.22), residues: 1541
  helix:  2.80 (0.14), residues: 1217
  sheet:  1.81 (0.97), residues: 24
  loop : -1.01 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 102 
 TYR   0.025   0.001   TYR D 160 
 PHE   0.019   0.001   PHE B 385 
 TRP   0.009   0.001   TRP B  13 
 HIS   0.004   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (13359)
  covalent geometry    : angle       0.47645 (18084)
  hydrogen bonds       : bond        0.04293 (  960)
  hydrogen bonds       : angle       3.30180 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 166
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A   98 LYS cc_start: 0.7835 (mptm) cc_final: 0.7300 (mmtt)
REVERT: A  178 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8444 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7672 (mp0)
REVERT: A  312 ARG cc_start: 0.8088 (ttt180) cc_final: 0.7743 (mtp180)
REVERT: A  384 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8045 (tpp)
REVERT: B   42 LYS cc_start: 0.7411 (mtpt) cc_final: 0.6920 (mmtt)
REVERT: B  178 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7951 (ttm170)
REVERT: B  199 PHE cc_start: 0.8418 (t80) cc_final: 0.8017 (t80)
REVERT: B  461 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6285 (tp40)
REVERT: B  462 LEU cc_start: 0.7206 (tt) cc_final: 0.6944 (mp)
REVERT: C   87 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.6940 (mmt)
REVERT: C  178 ARG cc_start: 0.7098 (ttm-80) cc_final: 0.6671 (ttm-80)
REVERT: C  216 MET cc_start: 0.7754 (mmp) cc_final: 0.7467 (mmt)
REVERT: C  401 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: D    5 ASP cc_start: 0.6851 (t0) cc_final: 0.6547 (t0)
REVERT: D   89 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7499 (mtm-85)
  outliers start: 37
  outliers final: 26
  residues processed: 192
  average time/residue: 0.5103
  time to fit residues: 107.9589
Evaluate side-chains
  192 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  407 HIS
Chi-restraints excluded: chain B residue  461 GLN
Chi-restraints excluded: chain C residue   22 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 82 optimal weight:    8.9990
   chunk 142 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0370
   chunk 99 optimal weight:    5.9990
   chunk 92 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 120 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   overall best weight:    0.9262

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
B 407 HIS
** D 240 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 = 0.3756 r_free = 0.3756 target = 0.150888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.104835 restraints weight = 15292.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 2.11
r_work: 0.3012 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13359  Z= 0.125
  Angle     :  0.474  13.038  18084  Z= 0.243
  Chirality :  0.037   0.227   2063
  Planarity :  0.003   0.055   2140
  Dihedral  : 10.284  89.417   2019
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.11 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.22 (0.22), residues: 1541
  helix:  2.82 (0.14), residues: 1217
  sheet:  1.88 (0.97), residues: 24
  loop : -0.97 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 102 
 TYR   0.029   0.001   TYR D 160 
 PHE   0.017   0.001   PHE B 385 
 TRP   0.010   0.001   TRP B 408 
 HIS   0.003   0.001   HIS A 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13359)
  covalent geometry    : angle       0.47367 (18084)
  hydrogen bonds       : bond        0.04175 (  960)
  hydrogen bonds       : angle       3.28970 ( 2862)

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

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

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3082 Ramachandran restraints generated.
    1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A   98 LYS cc_start: 0.8215 (mptm) cc_final: 0.7692 (mmtt)
REVERT: A  178 ARG cc_start: 0.8929 (ttm-80) cc_final: 0.8639 (ttm-80)
REVERT: A  229 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7872 (mp0)
REVERT: A  312 ARG cc_start: 0.8325 (ttt180) cc_final: 0.7938 (mtp180)
REVERT: A  384 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8239 (tpp)
REVERT: B   42 LYS cc_start: 0.7712 (mtpt) cc_final: 0.7141 (mmtt)
REVERT: B  178 ARG cc_start: 0.8458 (ttm170) cc_final: 0.8244 (ttm170)
REVERT: B  199 PHE cc_start: 0.8652 (t80) cc_final: 0.8255 (t80)
REVERT: B  462 LEU cc_start: 0.7302 (tt) cc_final: 0.7052 (mp)
REVERT: C   87 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7225 (mmt)
REVERT: C  129 SER cc_start: 0.7079 (t) cc_final: 0.6718 (m)
REVERT: C  178 ARG cc_start: 0.7164 (ttm-80) cc_final: 0.6771 (ttm-80)
REVERT: C  216 MET cc_start: 0.7905 (mmp) cc_final: 0.7621 (mmt)
REVERT: D    5 ASP cc_start: 0.6930 (t0) cc_final: 0.6622 (t0)
REVERT: D   89 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7645 (mtm-85)
  outliers start: 31
  outliers final: 25
  residues processed: 186
  average time/residue: 0.5621
  time to fit residues: 115.1938
Evaluate side-chains
  188 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  229 GLU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  324 HIS
Chi-restraints excluded: chain A residue  335 CYS
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain B residue   66 LYS
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  243 GLU
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain C residue   22 SER
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   87 MET
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  382 ILE
Chi-restraints excluded: chain C residue  399 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue   43 SER
Chi-restraints excluded: chain D residue   66 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  275 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 116 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 121 optimal weight:    2.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 212 HIS
B 407 HIS
D  46 HIS
D  86 GLN
** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.150827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.105157 restraints weight = 15145.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 2.08
r_work: 0.2962 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13359  Z= 0.123
  Angle     :  0.471  13.041  18084  Z= 0.242
  Chirality :  0.037   0.227   2063
  Planarity :  0.003   0.055   2140
  Dihedral  : 10.163  89.797   2019
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.04 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.25 (0.22), residues: 1541
  helix:  2.84 (0.14), residues: 1217
  sheet:  1.90 (0.97), residues: 24
  loop : -0.96 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 102 
 TYR   0.029   0.001   TYR D 160 
 PHE   0.017   0.001   PHE B 385 
 TRP   0.009   0.001   TRP B  13 
 HIS   0.006   0.001   HIS B 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (13359)
  covalent geometry    : angle       0.47106 (18084)
  hydrogen bonds       : bond        0.04145 (  960)
  hydrogen bonds       : angle       3.28369 ( 2862)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4720.44 seconds
wall clock time: 81 minutes 19.41 seconds (4879.41 seconds total)