Starting phenix.real_space_refine
on Sun Aug 24 02:53:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uhb_42268/08_2025/8uhb_42268_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uhb_42268/08_2025/8uhb_42268.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uhb_42268/08_2025/8uhb_42268_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uhb_42268/08_2025/8uhb_42268_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uhb_42268/08_2025/8uhb_42268.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uhb_42268/08_2025/8uhb_42268.map"
  }
  resolution = 3.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    5346      2.51       5
     N    1453      2.21       5
     O    1553      1.98       5
     H    8144      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16561
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 4754
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 11, 'TRANS': 304}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 140
          Unresolved non-hydrogen angles: 173
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'HIS:plan': 3, 'ASN:plan1': 4, 'GLU:plan': 2, 'TYR:plan': 2, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      Number of atoms: 5106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 5106
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 3890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 3890
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 884
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 1911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 1911
          Classifications: {'peptide': 128}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "A"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 16
          Unusual residues: {'WV8': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.32, per 1000 atoms: 0.20
  Number of scatterers: 16561
  At special positions: 0
  Unit cell: (85.52, 100.486, 136.832, 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      65     16.00
     O    1553      8.00
     N    1453      7.00
     C    5346      6.00
     H    8144      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   5 " - pdb=" SG  CYS A 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  13 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 182 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 471.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2026

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 12 sheets defined
      39.9% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 51
      removed outlier: 3.835A  pdb=" N   ILE A  48 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER A  49 " --> pdb=" O   ILE A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 76
      removed outlier: 3.918A  pdb=" N   ILE A  62 " --> pdb=" O   THR A  58 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER A  64 " --> pdb=" O   TRP A  60 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   THR A  67 " --> pdb=" O   HIS A  63 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A  68 " --> pdb=" O   SER A  64 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ASP A  69 " --> pdb=" O   MET A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 87
      removed outlier: 3.556A  pdb=" N   SER A  80 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ARG A  83 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 101
      removed outlier: 3.686A  pdb=" N   LYS A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ILE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 126
    Processing helix  chain 'A' and resid 130 through 135
      removed outlier: 3.506A  pdb=" N   LYS A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 157
      Proline residue:  A 151  - end of helix
    Processing helix  chain 'A' and resid 169 through 178
      removed outlier: 3.954A  pdb=" N   CYS A 178 " --> pdb=" O   LYS A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 199
    Processing helix  chain 'A' and resid 199 through 228
      removed outlier: 4.152A  pdb=" N   ARG A 212 " --> pdb=" O   CYS A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 278
      removed outlier: 4.272A  pdb=" N   LYS A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   PHE A 260 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      Proline residue:  A 266  - end of helix
      removed outlier: 3.725A  pdb=" N   ASP A 274 " --> pdb=" O   CYS A 270 " (cutoff:3.500A)
      Proline residue:  A 275  - end of helix
    Processing helix  chain 'A' and resid 282 through 305
      removed outlier: 3.693A  pdb=" N   ASN A 286 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER A 297 " --> pdb=" O   GLY A 293 " (cutoff:3.500A)
      Proline residue:  A 301  - end of helix
    Processing helix  chain 'A' and resid 308 through 319
    Processing helix  chain 'A' and resid 327 through 331
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.761A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.677A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 38
    Processing helix  chain 'C' and resid 55 through 60
    Processing helix  chain 'C' and resid 269 through 279
      removed outlier: 3.526A  pdb=" N   ASP C 274 " --> pdb=" O   LEU C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 303
    Processing helix  chain 'C' and resid 334 through 353
      removed outlier: 4.249A  pdb=" N   LYS C 338 " --> pdb=" O   VAL C 334 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG C 342 " --> pdb=" O   LYS C 338 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   GLU C 344 " --> pdb=" O   PHE C 340 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   PHE C 345 " --> pdb=" O   ILE C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 391
      removed outlier: 3.951A  pdb=" N   VAL C 375 " --> pdb=" O   ASN C 371 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ASP C 381 " --> pdb=" O   ASN C 377 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE C 383 " --> pdb=" O   CYS C 379 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 24
      removed outlier: 3.532A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'G' and resid 46 through 48
      No H-bonds generated for 'chain 'G' and resid 46 through 48'
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.673A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.986A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.984A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.617A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.162A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.715A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.809A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.471A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41
    Processing sheet with id=AA9, first strand: chain 'C' and resid 208 through 209
    Processing sheet with id=AB1, first strand: chain 'C' and resid 246 through 249
      removed outlier: 7.020A  pdb=" N   VAL C 287 " --> pdb=" O   TYR C 360 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   HIS C 362 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU C 289 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11
      removed outlier: 3.502A  pdb=" N   THR N 125 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1113 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: 3.56

  Time building geometry restraints manager: 2.07 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8118
        1.03 -     1.23: 141
        1.23 -     1.43: 3560
        1.43 -     1.62: 4828
        1.62 -     1.82: 94
  Bond restraints: 16741
  Sorted by residual:
  bond pdb=" C8  WV8 A 401 "
       pdb=" N9  WV8 A 401 "
    ideal  model  delta    sigma   weight residual
    1.359  1.326  0.033 2.00e-02 2.50e+03 2.74e+00
  bond pdb=" C   MET A  77 "
       pdb=" O   MET A  77 "
    ideal  model  delta    sigma   weight residual
    1.244  1.231  0.013 1.00e-02 1.00e+04 1.60e+00
  bond pdb=" CB  TRP B  99 "
       pdb=" CG  TRP B  99 "
    ideal  model  delta    sigma   weight residual
    1.498  1.468  0.030 3.10e-02 1.04e+03 9.30e-01
  bond pdb=" C   VAL A 250 "
       pdb=" O   VAL A 250 "
    ideal  model  delta    sigma   weight residual
    1.237  1.226  0.011 1.12e-02 7.97e+03 9.28e-01
  bond pdb=" C8  WV8 A 401 "
       pdb=" O7  WV8 A 401 "
    ideal  model  delta    sigma   weight residual
    1.361  1.344  0.017 2.00e-02 2.50e+03 6.90e-01
  ... (remaining 16736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 27324
        1.01 -     2.02: 2542
        2.02 -     3.03: 149
        3.03 -     4.04: 44
        4.04 -     5.05: 14
  Bond angle restraints: 30073
  Sorted by residual:
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     113.20  109.67    3.53 9.60e-01 1.09e+00 1.35e+01
  angle pdb=" N   ILE C 372 "
        pdb=" CA  ILE C 372 "
        pdb=" C   ILE C 372 "
      ideal   model   delta    sigma   weight residual
     112.35  107.30    5.05 1.41e+00 5.03e-01 1.28e+01
  angle pdb=" N   ILE C 235 "
        pdb=" CA  ILE C 235 "
        pdb=" C   ILE C 235 "
      ideal   model   delta    sigma   weight residual
     113.07  108.53    4.54 1.37e+00 5.33e-01 1.10e+01
  angle pdb=" N   ASP C 310 "
        pdb=" CA  ASP C 310 "
        pdb=" C   ASP C 310 "
      ideal   model   delta    sigma   weight residual
     114.04  110.13    3.91 1.24e+00 6.50e-01 9.93e+00
  angle pdb=" N   VAL A  46 "
        pdb=" CA  VAL A  46 "
        pdb=" C   VAL A  46 "
      ideal   model   delta    sigma   weight residual
     111.45  108.65    2.80 9.30e-01 1.16e+00 9.06e+00
  ... (remaining 30068 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 7184
       17.66 -    35.32: 599
       35.32 -    52.98: 135
       52.98 -    70.64: 21
       70.64 -    88.30: 9
  Dihedral angle restraints: 7948
    sinusoidal: 4200
      harmonic: 3748
  Sorted by residual:
  dihedral pdb=" CB  CYS A   5 "
           pdb=" SG  CYS A   5 "
           pdb=" SG  CYS A 178 "
           pdb=" CB  CYS A 178 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.02  -82.02     1      1.00e+01 1.00e-02 8.27e+01
  dihedral pdb=" CB  CYS A  96 "
           pdb=" SG  CYS A  96 "
           pdb=" SG  CYS A 182 "
           pdb=" CB  CYS A 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.02   68.02     1      1.00e+01 1.00e-02 6.01e+01
  dihedral pdb=" CA  ILE C 341 "
           pdb=" C   ILE C 341 "
           pdb=" N   ARG C 342 "
           pdb=" CA  ARG C 342 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.50   24.50     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 7945 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 787
       0.032 -    0.064: 371
       0.064 -    0.096: 94
       0.096 -    0.128: 44
       0.128 -    0.160: 8
  Chirality restraints: 1304
  Sorted by residual:
  chirality pdb=" CA  ILE C 341 "
            pdb=" N   ILE C 341 "
            pdb=" C   ILE C 341 "
            pdb=" CB  ILE C 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CB  VAL A  46 "
            pdb=" CA  VAL A  46 "
            pdb=" CG1 VAL A  46 "
            pdb=" CG2 VAL A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  ILE C 244 "
            pdb=" N   ILE C 244 "
            pdb=" C   ILE C 244 "
            pdb=" CB  ILE C 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  ... (remaining 1301 not shown)

  Planarity restraints: 2509
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5  WV8 A 401 "    0.048 2.00e-02 2.50e+03   3.77e-02 1.78e+01
        pdb=" C8  WV8 A 401 "   -0.013 2.00e-02 2.50e+03
        pdb=" N10 WV8 A 401 "   -0.051 2.00e-02 2.50e+03
        pdb=" N9  WV8 A 401 "    0.039 2.00e-02 2.50e+03
        pdb=" O7  WV8 A 401 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 234 "    0.020 2.00e-02 2.50e+03   1.16e-02 4.04e+00
        pdb=" CG  PHE B 234 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 234 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 234 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 234 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 234 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 234 "    0.003 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 234 "   -0.005 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 234 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 234 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 234 "    0.002 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 234 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 281 "    0.031 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO A 282 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 282 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 282 "    0.026 5.00e-02 4.00e+02
  ... (remaining 2506 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.06: 262
        2.06 -     2.69: 26322
        2.69 -     3.33: 47799
        3.33 -     3.96: 61919
        3.96 -     4.60: 97889
  Nonbonded interactions: 234191
  Sorted by model distance:
  nonbonded pdb=" HE2 HIS C 362 "
            pdb=" OD2 ASP C 378 "
     model   vdw
     1.420 2.450
  nonbonded pdb=" OD1 ASP C 331 "
            pdb=" H   VAL C 334 "
     model   vdw
     1.525 2.450
  nonbonded pdb=" OD1 ASP B 228 "
            pdb=" HH  TYR N 117 "
     model   vdw
     1.564 2.450
  nonbonded pdb=" O   ARG B  68 "
            pdb=" HG  SER B  84 "
     model   vdw
     1.606 2.450
  nonbonded pdb="HH12 ARG N  67 "
            pdb=" OD2 ASP N  90 "
     model   vdw
     1.630 2.450
  ... (remaining 234186 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  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:             0.110
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.780
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
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      :  0.004   0.034   8602  Z= 0.172
  Angle     :  0.621   5.054  11653  Z= 0.368
  Chirality :  0.041   0.160   1304
  Planarity :  0.003   0.048   1482
  Dihedral  : 14.115  88.305   3086
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.26), residues: 1059
  helix:  0.13 (0.28), residues: 385
  sheet: -1.84 (0.33), residues: 218
  loop : -1.30 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  19 
 TYR   0.013   0.001   TYR C 311 
 PHE   0.035   0.001   PHE B 234 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 8597)
  covalent geometry    : angle       0.61901 (11643)
  SS BOND              : bond        0.00167 (    5)
  SS BOND              : angle       1.80433 (   10)
  hydrogen bonds       : bond        0.15593 (  390)
  hydrogen bonds       : angle       7.43436 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  180 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  263 THR cc_start: 0.5105 (t) cc_final: 0.4902 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2736
  time to fit residues: 62.5862
Evaluate side-chains
  117 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  41 ASN
A  55 HIS
B  16 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.072126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.056014 restraints weight = 86682.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 4.28
r_work: 0.2879 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8602  Z= 0.188
  Angle     :  0.584   5.149  11653  Z= 0.321
  Chirality :  0.041   0.137   1304
  Planarity :  0.004   0.046   1482
  Dihedral  :  5.483  37.971   1183
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  7.92 %
    Favored  : 91.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (0.26), residues: 1059
  helix:  0.31 (0.27), residues: 399
  sheet: -1.74 (0.33), residues: 226
  loop : -1.32 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 283 
 TYR   0.009   0.001   TYR B 264 
 PHE   0.019   0.001   PHE B 234 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.006   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 8597)
  covalent geometry    : angle       0.58311 (11643)
  SS BOND              : bond        0.00141 (    5)
  SS BOND              : angle       1.27896 (   10)
  hydrogen bonds       : bond        0.04377 (  390)
  hydrogen bonds       : angle       5.58152 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 GLN cc_start: 0.9323 (mp10) cc_final: 0.8920 (pm20)
REVERT: A   81 MET cc_start: 0.9157 (ttm) cc_final: 0.8893 (ttm)
REVERT: A  158 MET cc_start: 0.9089 (tmm) cc_final: 0.8888 (tmm)
REVERT: B  246 ASP cc_start: 0.9243 (m-30) cc_final: 0.8977 (m-30)
REVERT: C  279 ASN cc_start: 0.9748 (t0) cc_final: 0.9283 (t0)
REVERT: G   21 MET cc_start: 0.9401 (ttt) cc_final: 0.9181 (ttm)
REVERT: N   34 MET cc_start: 0.8775 (mmm) cc_final: 0.8555 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 120
  average time/residue: 0.2242
  time to fit residues: 35.4099
Evaluate side-chains
  108 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain C residue   15 GLU
Chi-restraints excluded: chain C residue  379 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 55 optimal weight:    0.5980
   chunk 96 optimal weight:    3.9990
   overall best weight:    2.3188

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

Flipped N/Q/H residues before XYZ refinement:
** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.070167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.054226 restraints weight = 88248.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 4.22
r_work: 0.2844 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   8602  Z= 0.220
  Angle     :  0.568   6.830  11653  Z= 0.311
  Chirality :  0.040   0.132   1304
  Planarity :  0.004   0.040   1482
  Dihedral  :  5.204  33.646   1183
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.25 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.26), residues: 1059
  helix:  0.57 (0.27), residues: 400
  sheet: -1.44 (0.34), residues: 221
  loop : -1.29 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  96 
 TYR   0.010   0.001   TYR C 311 
 PHE   0.018   0.001   PHE C 222 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.006   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 8597)
  covalent geometry    : angle       0.56740 (11643)
  SS BOND              : bond        0.00079 (    5)
  SS BOND              : angle       0.79597 (   10)
  hydrogen bonds       : bond        0.04071 (  390)
  hydrogen bonds       : angle       5.25684 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.9077 (tmm) cc_final: 0.8860 (tmm)
REVERT: B  246 ASP cc_start: 0.9214 (m-30) cc_final: 0.8921 (m-30)
REVERT: B  322 ASP cc_start: 0.9078 (m-30) cc_final: 0.8754 (t0)
REVERT: C   15 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9239 (tm-30)
REVERT: C   60 MET cc_start: 0.8696 (mpp) cc_final: 0.8361 (mpp)
REVERT: C  268 GLU cc_start: 0.8800 (pt0) cc_final: 0.8483 (pt0)
REVERT: G   21 MET cc_start: 0.9399 (ttt) cc_final: 0.9125 (ttm)
REVERT: N   34 MET cc_start: 0.8798 (mmm) cc_final: 0.8565 (mmm)
  outliers start: 10
  outliers final: 7
  residues processed: 118
  average time/residue: 0.2125
  time to fit residues: 33.3801
Evaluate side-chains
  112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue   15 GLU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue   46 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 68 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.069931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.053987 restraints weight = 87471.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 4.19
r_work: 0.2838 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8602  Z= 0.182
  Angle     :  0.536   6.092  11653  Z= 0.293
  Chirality :  0.040   0.135   1304
  Planarity :  0.003   0.039   1482
  Dihedral  :  5.021  33.464   1183
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.14 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.27), residues: 1059
  helix:  0.86 (0.27), residues: 401
  sheet: -1.36 (0.33), residues: 228
  loop : -1.17 (0.32), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 118 
 TYR   0.012   0.001   TYR C 358 
 PHE   0.015   0.001   PHE C 212 
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS C 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 8597)
  covalent geometry    : angle       0.53611 (11643)
  SS BOND              : bond        0.00082 (    5)
  SS BOND              : angle       0.66065 (   10)
  hydrogen bonds       : bond        0.03758 (  390)
  hydrogen bonds       : angle       5.05361 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.9061 (tmm) cc_final: 0.8838 (tmm)
REVERT: B  246 ASP cc_start: 0.9199 (m-30) cc_final: 0.8880 (m-30)
REVERT: B  322 ASP cc_start: 0.9075 (m-30) cc_final: 0.8806 (t0)
REVERT: C   15 GLU cc_start: 0.9492 (OUTLIER) cc_final: 0.9252 (tm-30)
REVERT: C   60 MET cc_start: 0.8697 (mpp) cc_final: 0.8480 (mpp)
REVERT: G   21 MET cc_start: 0.9433 (ttt) cc_final: 0.9177 (ttm)
REVERT: N   34 MET cc_start: 0.8836 (mmm) cc_final: 0.8437 (tpp)
REVERT: N   35 ASN cc_start: 0.8723 (m-40) cc_final: 0.8476 (m-40)
  outliers start: 12
  outliers final: 8
  residues processed: 118
  average time/residue: 0.2190
  time to fit residues: 34.6136
Evaluate side-chains
  112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue   15 GLU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  390 GLN
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue  107 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 31 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.069225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.053531 restraints weight = 87680.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 4.16
r_work: 0.2843 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8602  Z= 0.173
  Angle     :  0.528   5.472  11653  Z= 0.288
  Chirality :  0.039   0.135   1304
  Planarity :  0.003   0.038   1482
  Dihedral  :  4.896  33.753   1183
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 11.37 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.27), residues: 1059
  helix:  1.10 (0.27), residues: 398
  sheet: -1.25 (0.34), residues: 216
  loop : -1.20 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 118 
 TYR   0.007   0.001   TYR C 358 
 PHE   0.013   0.001   PHE C 212 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8597)
  covalent geometry    : angle       0.52838 (11643)
  SS BOND              : bond        0.00129 (    5)
  SS BOND              : angle       0.60008 (   10)
  hydrogen bonds       : bond        0.03654 (  390)
  hydrogen bonds       : angle       4.92216 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.9311 (m-30) cc_final: 0.9029 (t0)
REVERT: A  158 MET cc_start: 0.9040 (tmm) cc_final: 0.8826 (tmm)
REVERT: B  246 ASP cc_start: 0.9192 (m-30) cc_final: 0.8880 (m-30)
REVERT: B  322 ASP cc_start: 0.9067 (m-30) cc_final: 0.8815 (t0)
REVERT: C   15 GLU cc_start: 0.9491 (OUTLIER) cc_final: 0.9265 (tm-30)
REVERT: C   60 MET cc_start: 0.8624 (mpp) cc_final: 0.8365 (mpp)
REVERT: G   21 MET cc_start: 0.9404 (ttt) cc_final: 0.9152 (ttm)
REVERT: N   34 MET cc_start: 0.8850 (mmm) cc_final: 0.8439 (tpp)
REVERT: N   35 ASN cc_start: 0.8696 (m-40) cc_final: 0.8457 (m-40)
  outliers start: 8
  outliers final: 7
  residues processed: 114
  average time/residue: 0.2525
  time to fit residues: 38.7003
Evaluate side-chains
  111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue   15 GLU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue  107 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.068817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.053476 restraints weight = 88280.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 4.15
r_work: 0.2833 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8602  Z= 0.190
  Angle     :  0.534   5.205  11653  Z= 0.291
  Chirality :  0.039   0.135   1304
  Planarity :  0.003   0.037   1482
  Dihedral  :  4.827  33.863   1183
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.26 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.27), residues: 1059
  helix:  1.31 (0.27), residues: 401
  sheet: -1.15 (0.34), residues: 221
  loop : -1.13 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N 118 
 TYR   0.010   0.001   TYR C 358 
 PHE   0.013   0.001   PHE C 212 
 TRP   0.015   0.001   TRP B  82 
 HIS   0.005   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8597)
  covalent geometry    : angle       0.53406 (11643)
  SS BOND              : bond        0.00106 (    5)
  SS BOND              : angle       0.62821 (   10)
  hydrogen bonds       : bond        0.03598 (  390)
  hydrogen bonds       : angle       4.84531 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  120 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 MET cc_start: 0.9060 (tmm) cc_final: 0.8856 (tmm)
REVERT: B  246 ASP cc_start: 0.9188 (m-30) cc_final: 0.8861 (m-30)
REVERT: B  322 ASP cc_start: 0.9076 (m-30) cc_final: 0.8810 (t0)
REVERT: C   60 MET cc_start: 0.8540 (mpp) cc_final: 0.8241 (mpp)
REVERT: G   21 MET cc_start: 0.9391 (ttt) cc_final: 0.9136 (ttm)
REVERT: N   34 MET cc_start: 0.8853 (mmm) cc_final: 0.8410 (tpp)
REVERT: N   35 ASN cc_start: 0.8664 (m-40) cc_final: 0.8410 (m-40)
  outliers start: 13
  outliers final: 11
  residues processed: 117
  average time/residue: 0.2245
  time to fit residues: 34.6023
Evaluate side-chains
  112 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  296 ASN
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue   15 GLU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain C residue  390 GLN
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  120 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0770
   chunk 27 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.7342

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.069714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.054129 restraints weight = 87772.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 4.17
r_work: 0.2858 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8602  Z= 0.113
  Angle     :  0.523   5.595  11653  Z= 0.280
  Chirality :  0.039   0.135   1304
  Planarity :  0.003   0.037   1482
  Dihedral  :  4.747  34.549   1183
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.10 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 12.49 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.27), residues: 1059
  helix:  1.42 (0.27), residues: 398
  sheet: -0.98 (0.34), residues: 215
  loop : -1.06 (0.32), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 389 
 TYR   0.009   0.001   TYR A 200 
 PHE   0.016   0.001   PHE C 222 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8597)
  covalent geometry    : angle       0.52129 (11643)
  SS BOND              : bond        0.00089 (    5)
  SS BOND              : angle       1.65575 (   10)
  hydrogen bonds       : bond        0.03475 (  390)
  hydrogen bonds       : angle       4.71685 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.9439 (m-30) cc_final: 0.9214 (t0)
REVERT: A  158 MET cc_start: 0.9048 (tmm) cc_final: 0.8843 (tmm)
REVERT: B  246 ASP cc_start: 0.9174 (m-30) cc_final: 0.8829 (m-30)
REVERT: B  322 ASP cc_start: 0.9023 (m-30) cc_final: 0.8769 (t0)
REVERT: C  221 MET cc_start: 0.8705 (tpp) cc_final: 0.8413 (tpp)
REVERT: G   21 MET cc_start: 0.9408 (ttt) cc_final: 0.9163 (ttm)
REVERT: N   34 MET cc_start: 0.8887 (mmm) cc_final: 0.8449 (tpp)
REVERT: N   35 ASN cc_start: 0.8631 (m-40) cc_final: 0.8384 (m-40)
  outliers start: 8
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1871
  time to fit residues: 30.1120
Evaluate side-chains
  110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue  379 CYS
Chi-restraints excluded: chain N residue  107 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 91 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 70 optimal weight:    0.4980
   chunk 7 optimal weight:    0.2980
   chunk 82 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 55 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:
** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.070844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.055297 restraints weight = 86794.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 4.12
r_work: 0.2888 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8602  Z= 0.132
  Angle     :  0.531   5.694  11653  Z= 0.284
  Chirality :  0.039   0.133   1304
  Planarity :  0.003   0.035   1482
  Dihedral  :  4.694  34.718   1183
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 13.60 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.27), residues: 1059
  helix:  1.50 (0.27), residues: 398
  sheet: -0.82 (0.35), residues: 210
  loop : -1.07 (0.31), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.013   0.001   TYR B 264 
 PHE   0.014   0.001   PHE C 222 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8597)
  covalent geometry    : angle       0.52996 (11643)
  SS BOND              : bond        0.00232 (    5)
  SS BOND              : angle       1.46459 (   10)
  hydrogen bonds       : bond        0.03430 (  390)
  hydrogen bonds       : angle       4.73486 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.9416 (m-30) cc_final: 0.9190 (t0)
REVERT: B  246 ASP cc_start: 0.9135 (m-30) cc_final: 0.8806 (m-30)
REVERT: B  322 ASP cc_start: 0.8961 (m-30) cc_final: 0.8746 (t0)
REVERT: C  221 MET cc_start: 0.8691 (tpp) cc_final: 0.8409 (tpp)
REVERT: G   21 MET cc_start: 0.9395 (ttt) cc_final: 0.9148 (ttm)
REVERT: G   47 GLU cc_start: 0.8939 (mp0) cc_final: 0.8541 (mp0)
REVERT: N   34 MET cc_start: 0.8903 (mmm) cc_final: 0.8503 (tpp)
REVERT: N   35 ASN cc_start: 0.8647 (m-40) cc_final: 0.8366 (m-40)
REVERT: N   77 ASN cc_start: 0.9249 (m-40) cc_final: 0.8878 (p0)
  outliers start: 6
  outliers final: 4
  residues processed: 110
  average time/residue: 0.2447
  time to fit residues: 35.9672
Evaluate side-chains
  108 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain N residue  107 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 101 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.070589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.055365 restraints weight = 87664.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 4.05
r_work: 0.2886 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8602  Z= 0.165
  Angle     :  0.540   5.790  11653  Z= 0.291
  Chirality :  0.040   0.137   1304
  Planarity :  0.003   0.035   1482
  Dihedral  :  4.678  34.677   1183
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 13.04 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.27), residues: 1059
  helix:  1.52 (0.27), residues: 398
  sheet: -0.95 (0.34), residues: 224
  loop : -1.03 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.010   0.001   TYR A 210 
 PHE   0.012   0.001   PHE C 222 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.005   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 8597)
  covalent geometry    : angle       0.53929 (11643)
  SS BOND              : bond        0.00224 (    5)
  SS BOND              : angle       0.97927 (   10)
  hydrogen bonds       : bond        0.03437 (  390)
  hydrogen bonds       : angle       4.70951 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  246 ASP cc_start: 0.9138 (m-30) cc_final: 0.8790 (m-30)
REVERT: B  322 ASP cc_start: 0.8995 (m-30) cc_final: 0.8757 (t0)
REVERT: C  221 MET cc_start: 0.8767 (tpp) cc_final: 0.8464 (tpp)
REVERT: N   34 MET cc_start: 0.8880 (mmm) cc_final: 0.8467 (tpp)
REVERT: N   35 ASN cc_start: 0.8603 (m-40) cc_final: 0.8298 (m-40)
REVERT: N   77 ASN cc_start: 0.9292 (m-40) cc_final: 0.8885 (p0)
  outliers start: 8
  outliers final: 7
  residues processed: 112
  average time/residue: 0.2533
  time to fit residues: 37.6981
Evaluate side-chains
  107 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  120 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 11 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.070267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.054831 restraints weight = 86876.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 4.07
r_work: 0.2910 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8602  Z= 0.162
  Angle     :  0.540   5.871  11653  Z= 0.291
  Chirality :  0.039   0.132   1304
  Planarity :  0.003   0.035   1482
  Dihedral  :  4.699  35.514   1183
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.15 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.27), residues: 1059
  helix:  1.54 (0.27), residues: 398
  sheet: -0.91 (0.34), residues: 224
  loop : -1.03 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 121 
 TYR   0.009   0.001   TYR B 264 
 PHE   0.012   0.001   PHE C 222 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8597)
  covalent geometry    : angle       0.53907 (11643)
  SS BOND              : bond        0.00178 (    5)
  SS BOND              : angle       1.00040 (   10)
  hydrogen bonds       : bond        0.03434 (  390)
  hydrogen bonds       : angle       4.71307 ( 1113)

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

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

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2118 Ramachandran restraints generated.
    1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE    8 is missing expected H atoms. Skipping.
Residue ILE    9 is missing expected H atoms. Skipping.
Residue ILE   11 is missing expected H atoms. Skipping.
Residue SER   12 is missing expected H atoms. Skipping.
Residue VAL   14 is missing expected H atoms. Skipping.
Residue LYS   15 is missing expected H atoms. Skipping.
Residue SER   19 is missing expected H atoms. Skipping.
Residue LYS   52 is missing expected H atoms. Skipping.
Residue ILE  171 is missing expected H atoms. Skipping.
Residue TYR  172 is missing expected H atoms. Skipping.
Residue TYR  173 is missing expected H atoms. Skipping.
Residue LYS  174 is missing expected H atoms. Skipping.
Residue VAL  176 is missing expected H atoms. Skipping.
Residue LYS  251 is missing expected H atoms. Skipping.
Residue MET  273 is missing expected H atoms. Skipping.
Residue ILE  280 is missing expected H atoms. Skipping.
Residue LYS  326 is missing expected H atoms. Skipping.
Residue SER  328 is missing expected H atoms. Skipping.
Residue SER  329 is missing expected H atoms. Skipping.
Residue LYS  332 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 MET cc_start: 0.9651 (OUTLIER) cc_final: 0.9328 (ttm)
REVERT: B  246 ASP cc_start: 0.9177 (m-30) cc_final: 0.8817 (m-30)
REVERT: B  262 MET cc_start: 0.9009 (ttm) cc_final: 0.8638 (ttm)
REVERT: B  322 ASP cc_start: 0.9012 (m-30) cc_final: 0.8746 (t0)
REVERT: C  221 MET cc_start: 0.8756 (tpp) cc_final: 0.8436 (tpp)
REVERT: N   34 MET cc_start: 0.8812 (mmm) cc_final: 0.8386 (tpp)
REVERT: N   35 ASN cc_start: 0.8535 (m-40) cc_final: 0.8197 (m-40)
REVERT: N   77 ASN cc_start: 0.9321 (m-40) cc_final: 0.8888 (p0)
  outliers start: 7
  outliers final: 6
  residues processed: 111
  average time/residue: 0.2399
  time to fit residues: 35.9297
Evaluate side-chains
  110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   81 MET
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain B residue   12 GLU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain N residue  107 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 90 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** C 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.070656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.055418 restraints weight = 87307.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 4.06
r_work: 0.2919 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8602  Z= 0.141
  Angle     :  0.529   5.668  11653  Z= 0.285
  Chirality :  0.039   0.131   1304
  Planarity :  0.003   0.036   1482
  Dihedral  :  4.643  35.838   1183
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 13.15 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.27), residues: 1059
  helix:  1.54 (0.26), residues: 404
  sheet: -0.80 (0.34), residues: 222
  loop : -0.95 (0.32), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 121 
 TYR   0.010   0.001   TYR C 358 
 PHE   0.011   0.001   PHE C 222 
 TRP   0.014   0.001   TRP B  82 
 HIS   0.005   0.001   HIS C 357 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8597)
  covalent geometry    : angle       0.52841 (11643)
  SS BOND              : bond        0.00178 (    5)
  SS BOND              : angle       0.80703 (   10)
  hydrogen bonds       : bond        0.03380 (  390)
  hydrogen bonds       : angle       4.66943 ( 1113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3233.16 seconds
wall clock time: 55 minutes 52.49 seconds (3352.49 seconds total)