Starting phenix.real_space_refine
on Tue Mar  3 16:08:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvu_32858/03_2026/7wvu_32858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvu_32858/03_2026/7wvu_32858.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvu_32858/03_2026/7wvu_32858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvu_32858/03_2026/7wvu_32858.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvu_32858/03_2026/7wvu_32858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvu_32858/03_2026/7wvu_32858.cif"
  }
  resolution = 3.3
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4405      2.51       5
     N    1157      2.21       5
     O    1250      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6862
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "R"
      Number of atoms: 2279
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2279
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 12, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1714
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2457
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2457
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 92
    Chain: "C"
      Number of atoms: 382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 382
          Classifications: {'peptide': 54}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "L"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 30
          Classifications: {'peptide': 3}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.59, per 1000 atoms: 0.23
  Number of scatterers: 6862
  At special positions: 0
  Unit cell: (113.905, 117.04, 80.465, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1250      8.00
     N    1157      7.00
     C    4405      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 263.6 milliseconds
  

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1710

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      48.8% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 53
    Processing helix  chain 'R' and resid 58 through 88
      removed outlier: 3.514A  pdb=" N   PHE R  74 " --> pdb=" O   ALA R  70 " (cutoff:3.500A)
      Proline residue:  R  79  - end of helix
      removed outlier: 3.644A  pdb=" N   ARG R  84 " --> pdb=" O   PHE R  80 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 94 through 129
      removed outlier: 3.808A  pdb=" N   ASP R 106 " --> pdb=" O   PHE R 102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 136
    Processing helix  chain 'R' and resid 138 through 163
      removed outlier: 3.659A  pdb=" N   ILE R 147 " --> pdb=" O   LYS R 143 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY R 148 " --> pdb=" O   LYS R 144 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 186 through 211
    Processing helix  chain 'R' and resid 212 through 231
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 272
    Processing helix  chain 'R' and resid 276 through 302
      removed outlier: 3.632A  pdb=" N   ASN R 293 " --> pdb=" O   LEU R 289 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   SER R 294 " --> pdb=" O   ALA R 290 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   CYS R 295 " --> pdb=" O   PHE R 291 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 305 through 316
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.600A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 53
      removed outlier: 4.070A  pdb=" N   CYS A  47 " --> pdb=" O   GLU A  43 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   THR A  48 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   MET A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 218
      removed outlier: 4.128A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   GLY A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.886A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.768A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.885A  pdb=" N   CYS A 286 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 4.367A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 3.663A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE A 334 " --> pdb=" O   LYS A 330 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.606A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR B  34 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 29 through 34'
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 10 through 22
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.620A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.509A  pdb=" N   LEU A  38 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.612A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TYR A 320 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.762A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.815A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.618A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 4.191A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.624A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 5.922A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1110 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2206
        1.34 -     1.46: 1622
        1.46 -     1.58: 3108
        1.58 -     1.70: 0
        1.70 -     1.81: 70
  Bond restraints: 7006
  Sorted by residual:
  bond pdb=" SD  FME L   1 "
       pdb=" CE  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.752  0.053 2.00e-02 2.50e+03 7.06e+00
  bond pdb=" CG  FME L   1 "
       pdb=" SD  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.772  0.045 2.00e-02 2.50e+03 5.03e+00
  bond pdb=" N   FME L   1 "
       pdb=" CN  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.375 -0.040 2.00e-02 2.50e+03 3.97e+00
  bond pdb=" N   FME L   1 "
       pdb=" CA  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.436  0.022 1.90e-02 2.77e+03 1.33e+00
  bond pdb=" C   ALA R 212 "
       pdb=" N   PRO R 213 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.09e+00
  ... (remaining 7001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 9410
        1.65 -     3.30: 99
        3.30 -     4.94: 15
        4.94 -     6.59: 5
        6.59 -     8.24: 1
  Bond angle restraints: 9530
  Sorted by residual:
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  127.78   -6.24 1.91e+00 2.74e-01 1.07e+01
  angle pdb=" CA  LEU R  39 "
        pdb=" CB  LEU R  39 "
        pdb=" CG  LEU R  39 "
      ideal   model   delta    sigma   weight residual
     116.30  124.54   -8.24 3.50e+00 8.16e-02 5.54e+00
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     121.54  125.96   -4.42 1.91e+00 2.74e-01 5.36e+00
  angle pdb=" C   PHE R 102 "
        pdb=" N   THR R 103 "
        pdb=" CA  THR R 103 "
      ideal   model   delta    sigma   weight residual
     121.64  117.20    4.44 2.13e+00 2.20e-01 4.34e+00
  angle pdb=" CB  GLN A 333 "
        pdb=" CG  GLN A 333 "
        pdb=" CD  GLN A 333 "
      ideal   model   delta    sigma   weight residual
     112.60  115.84   -3.24 1.70e+00 3.46e-01 3.63e+00
  ... (remaining 9525 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 3749
       17.71 -    35.41: 280
       35.41 -    53.12: 60
       53.12 -    70.82: 6
       70.82 -    88.52: 5
  Dihedral angle restraints: 4100
    sinusoidal: 1466
      harmonic: 2634
  Sorted by residual:
  dihedral pdb=" CB  CYS R  98 "
           pdb=" SG  CYS R  98 "
           pdb=" SG  CYS R 176 "
           pdb=" CB  CYS R 176 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -171.88   85.88     1      1.00e+01 1.00e-02 8.91e+01
  dihedral pdb=" CG  ARG B 150 "
           pdb=" CD  ARG B 150 "
           pdb=" NE  ARG B 150 "
           pdb=" CZ  ARG B 150 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -130.97   40.97     2      1.50e+01 4.44e-03 9.17e+00
  dihedral pdb=" CA  ARG R 269 "
           pdb=" CB  ARG R 269 "
           pdb=" CG  ARG R 269 "
           pdb=" CD  ARG R 269 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  127.00   53.00     3      1.50e+01 4.44e-03 9.17e+00
  ... (remaining 4097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 725
       0.029 -    0.058: 262
       0.058 -    0.087: 86
       0.087 -    0.117: 47
       0.117 -    0.146: 6
  Chirality restraints: 1126
  Sorted by residual:
  chirality pdb=" CB  VAL R 164 "
            pdb=" CA  VAL R 164 "
            pdb=" CG1 VAL R 164 "
            pdb=" CG2 VAL R 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.31e-01
  chirality pdb=" CA  ASN B 119 "
            pdb=" N   ASN B 119 "
            pdb=" C   ASN B 119 "
            pdb=" CB  ASN B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  ILE B  93 "
            pdb=" N   ILE B  93 "
            pdb=" C   ILE B  93 "
            pdb=" CB  ILE B  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 1123 not shown)

  Planarity restraints: 1199
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.061 5.00e-02 4.00e+02   9.23e-02 1.36e+01
        pdb=" N   PRO B 236 "   -0.160 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 148 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO R 149 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO R 149 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO R 149 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 287 "    0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO A 288 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1196 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 932
        2.76 -     3.29: 6734
        3.29 -     3.83: 11596
        3.83 -     4.36: 12952
        4.36 -     4.90: 23359
  Nonbonded interactions: 55573
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OH  TYR R 257 "
            pdb=" O   LEU L   2 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG  SER B 108 "
            pdb=" OD1 ASN B 110 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.333 3.040
  ... (remaining 55568 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:             1.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.410
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
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      :  0.002   0.053   7007  Z= 0.109
  Angle     :  0.466   8.238   9532  Z= 0.252
  Chirality :  0.038   0.146   1126
  Planarity :  0.004   0.092   1199
  Dihedral  : 13.254  88.524   2387
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.29), residues: 894
  helix:  2.27 (0.26), residues: 397
  sheet:  0.29 (0.43), residues: 155
  loop : -1.17 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 251 
 TYR   0.005   0.001   TYR B 264 
 PHE   0.009   0.001   PHE B 151 
 TRP   0.007   0.001   TRP R  49 
 HIS   0.001   0.000   HIS R 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 7006)
  covalent geometry    : angle       0.46625 ( 9530)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.43387 (    2)
  hydrogen bonds       : bond        0.18822 (  388)
  hydrogen bonds       : angle       6.66226 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B  191 SER cc_start: 0.8220 (p) cc_final: 0.8020 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0621
  time to fit residues: 11.9235
Evaluate side-chains
  112 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
** R  44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
A 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.182313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.144471 restraints weight = 7100.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 1.91
r_work: 0.3600 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3451 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7007  Z= 0.118
  Angle     :  0.507   6.861   9532  Z= 0.263
  Chirality :  0.040   0.137   1126
  Planarity :  0.004   0.064   1199
  Dihedral  :  4.328  77.680    963
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  9.69 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.29), residues: 894
  helix:  2.44 (0.26), residues: 402
  sheet:  0.12 (0.41), residues: 161
  loop : -1.10 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 251 
 TYR   0.010   0.001   TYR A 296 
 PHE   0.012   0.001   PHE R  93 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7006)
  covalent geometry    : angle       0.50706 ( 9530)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.25512 (    2)
  hydrogen bonds       : bond        0.03980 (  388)
  hydrogen bonds       : angle       4.95091 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8014 (t0) cc_final: 0.7705 (m-30)
REVERT: A  309 ASP cc_start: 0.7399 (m-30) cc_final: 0.7184 (m-30)
  outliers start: 10
  outliers final: 4
  residues processed: 123
  average time/residue: 0.0556
  time to fit residues: 10.0524
Evaluate side-chains
  111 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 83 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0570
   chunk 5 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 60 optimal weight:    0.1980
   chunk 76 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
** R  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.176888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.137863 restraints weight = 7128.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 1.94
r_work: 0.3535 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7007  Z= 0.114
  Angle     :  0.497   7.016   9532  Z= 0.252
  Chirality :  0.040   0.136   1126
  Planarity :  0.004   0.052   1199
  Dihedral  :  4.338  75.825    963
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.54 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.29), residues: 894
  helix:  2.42 (0.26), residues: 403
  sheet:  0.15 (0.41), residues: 158
  loop : -1.12 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 251 
 TYR   0.009   0.001   TYR R 257 
 PHE   0.010   0.001   PHE A 250 
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 7006)
  covalent geometry    : angle       0.49693 ( 9530)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       0.55993 (    2)
  hydrogen bonds       : bond        0.03534 (  388)
  hydrogen bonds       : angle       4.63427 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.283 
Fit side-chains
REVERT: R   87 MET cc_start: 0.5348 (mmt) cc_final: 0.5113 (mmt)
REVERT: R  152 MET cc_start: 0.6373 (tpt) cc_final: 0.5940 (tpt)
REVERT: R  276 TYR cc_start: 0.6664 (m-10) cc_final: 0.6215 (m-80)
REVERT: A  309 ASP cc_start: 0.7536 (m-30) cc_final: 0.7331 (m-30)
REVERT: B  254 ASP cc_start: 0.7132 (t70) cc_final: 0.6842 (t70)
  outliers start: 11
  outliers final: 10
  residues processed: 117
  average time/residue: 0.0679
  time to fit residues: 11.4367
Evaluate side-chains
  111 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 84 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0270
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
R 293 ASN
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
A 311 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.174245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134660 restraints weight = 7178.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 1.95
r_work: 0.3473 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7007  Z= 0.129
  Angle     :  0.499   7.382   9532  Z= 0.255
  Chirality :  0.040   0.131   1126
  Planarity :  0.004   0.049   1199
  Dihedral  :  4.474  76.906    963
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 13.39 %
    Favored  : 83.90 %
  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 are not related in a simple way.
  whole:  1.00 (0.29), residues: 894
  helix:  2.31 (0.26), residues: 404
  sheet: -0.12 (0.41), residues: 165
  loop : -1.04 (0.33), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 251 
 TYR   0.009   0.001   TYR B  59 
 PHE   0.011   0.001   PHE A 250 
 TRP   0.016   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7006)
  covalent geometry    : angle       0.49915 ( 9530)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.34269 (    2)
  hydrogen bonds       : bond        0.03460 (  388)
  hydrogen bonds       : angle       4.59277 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.218 
Fit side-chains
REVERT: R   54 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.7061 (mmt180)
REVERT: R  152 MET cc_start: 0.6497 (tpt) cc_final: 0.6112 (tpt)
REVERT: R  276 TYR cc_start: 0.6929 (m-10) cc_final: 0.6721 (m-10)
REVERT: B  254 ASP cc_start: 0.7337 (t70) cc_final: 0.7039 (t70)
  outliers start: 19
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0668
  time to fit residues: 10.8797
Evaluate side-chains
  109 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 83 optimal weight:   20.0000
   chunk 4 optimal weight:    0.0060
   chunk 17 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.1802

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.168207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129000 restraints weight = 7313.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.05
r_work: 0.3405 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7007  Z= 0.178
  Angle     :  0.554   7.479   9532  Z= 0.281
  Chirality :  0.042   0.137   1126
  Planarity :  0.004   0.048   1199
  Dihedral  :  4.769  78.680    963
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 14.25 %
    Favored  : 82.19 %
  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 are not related in a simple way.
  whole:  0.76 (0.29), residues: 894
  helix:  2.13 (0.26), residues: 397
  sheet: -0.31 (0.41), residues: 164
  loop : -1.08 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 123 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.013   0.002   PHE R  96 
 TRP   0.034   0.002   TRP B 339 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 7006)
  covalent geometry    : angle       0.55426 ( 9530)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.54826 (    2)
  hydrogen bonds       : bond        0.03701 (  388)
  hydrogen bonds       : angle       4.70740 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.223 
Fit side-chains
REVERT: R   54 ARG cc_start: 0.7356 (mmm-85) cc_final: 0.6665 (mmt180)
REVERT: R  152 MET cc_start: 0.6902 (tpt) cc_final: 0.6620 (tpt)
REVERT: R  276 TYR cc_start: 0.6973 (m-10) cc_final: 0.6698 (m-80)
REVERT: B  254 ASP cc_start: 0.7458 (t70) cc_final: 0.7148 (t70)
REVERT: B  259 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7227 (pm20)
REVERT: B  262 MET cc_start: 0.7333 (mmt) cc_final: 0.6861 (mmt)
  outliers start: 25
  outliers final: 22
  residues processed: 131
  average time/residue: 0.0672
  time to fit residues: 12.5333
Evaluate side-chains
  129 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 47 optimal weight:    0.4980
   chunk 75 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R  57 HIS
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.169718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.130462 restraints weight = 7384.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 2.07
r_work: 0.3418 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7007  Z= 0.144
  Angle     :  0.538   7.866   9532  Z= 0.272
  Chirality :  0.041   0.132   1126
  Planarity :  0.004   0.047   1199
  Dihedral  :  4.680  76.293    963
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 16.10 %
    Favored  : 79.91 %
  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 are not related in a simple way.
  whole:  0.74 (0.29), residues: 894
  helix:  2.14 (0.26), residues: 397
  sheet: -0.46 (0.40), residues: 166
  loop : -1.04 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  52 
 TYR   0.014   0.001   TYR B  59 
 PHE   0.013   0.001   PHE R 210 
 TRP   0.029   0.002   TRP B 339 
 HIS   0.003   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7006)
  covalent geometry    : angle       0.53794 ( 9530)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.26340 (    2)
  hydrogen bonds       : bond        0.03555 (  388)
  hydrogen bonds       : angle       4.73123 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.254 
Fit side-chains
REVERT: R   54 ARG cc_start: 0.7364 (mmm-85) cc_final: 0.6721 (mmt180)
REVERT: R  152 MET cc_start: 0.6929 (tpt) cc_final: 0.6676 (tpt)
REVERT: R  276 TYR cc_start: 0.6998 (m-10) cc_final: 0.6699 (m-80)
REVERT: B  138 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7975 (mt-10)
  outliers start: 28
  outliers final: 22
  residues processed: 124
  average time/residue: 0.0696
  time to fit residues: 12.3691
Evaluate side-chains
  125 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  209 LYS
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0770
   chunk 12 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0870
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 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 = 0.4080 r_free = 0.4080 target = 0.172328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.133188 restraints weight = 7246.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.91
r_work: 0.3468 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3317 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7007  Z= 0.117
  Angle     :  0.513   8.182   9532  Z= 0.259
  Chirality :  0.040   0.133   1126
  Planarity :  0.003   0.047   1199
  Dihedral  :  4.552  74.184    963
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.24 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.29), residues: 894
  helix:  2.20 (0.26), residues: 399
  sheet: -0.59 (0.41), residues: 158
  loop : -1.00 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  52 
 TYR   0.011   0.001   TYR A 296 
 PHE   0.009   0.001   PHE R 210 
 TRP   0.026   0.002   TRP B 339 
 HIS   0.002   0.000   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7006)
  covalent geometry    : angle       0.51330 ( 9530)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       0.10806 (    2)
  hydrogen bonds       : bond        0.03370 (  388)
  hydrogen bonds       : angle       4.61693 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.286 
Fit side-chains
REVERT: R   54 ARG cc_start: 0.7275 (mmm-85) cc_final: 0.6702 (mmt180)
REVERT: R  152 MET cc_start: 0.6853 (tpt) cc_final: 0.6622 (tpt)
REVERT: R  303 PHE cc_start: 0.7956 (m-10) cc_final: 0.7665 (m-10)
REVERT: A   53 MET cc_start: 0.6202 (pmm) cc_final: 0.5434 (pmm)
REVERT: B  138 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7897 (mt-10)
REVERT: B  254 ASP cc_start: 0.7386 (t70) cc_final: 0.7099 (t70)
  outliers start: 23
  outliers final: 20
  residues processed: 118
  average time/residue: 0.0671
  time to fit residues: 11.4315
Evaluate side-chains
  121 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 80 optimal weight:    0.0170
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:   10.0000
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 27 optimal weight:    0.1980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
A 311 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.172270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.133530 restraints weight = 7307.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 1.91
r_work: 0.3472 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7007  Z= 0.119
  Angle     :  0.511   8.170   9532  Z= 0.259
  Chirality :  0.040   0.134   1126
  Planarity :  0.003   0.046   1199
  Dihedral  :  4.538  74.580    963
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.95 %
    Favored  : 79.91 %
  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 are not related in a simple way.
  whole:  0.81 (0.29), residues: 894
  helix:  2.23 (0.26), residues: 399
  sheet: -0.63 (0.41), residues: 160
  loop : -0.94 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.010   0.001   TYR R 257 
 PHE   0.009   0.001   PHE A 274 
 TRP   0.026   0.001   TRP B 339 
 HIS   0.002   0.000   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7006)
  covalent geometry    : angle       0.51124 ( 9530)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.18424 (    2)
  hydrogen bonds       : bond        0.03337 (  388)
  hydrogen bonds       : angle       4.56276 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.244 
Fit side-chains
REVERT: R   54 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.6690 (mmt180)
REVERT: R  152 MET cc_start: 0.6873 (tpt) cc_final: 0.6656 (tpt)
REVERT: R  229 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6738 (t-90)
REVERT: R  303 PHE cc_start: 0.7986 (m-10) cc_final: 0.7696 (m-10)
REVERT: A   53 MET cc_start: 0.6288 (pmm) cc_final: 0.5426 (pmm)
REVERT: B  127 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8298 (mmtp)
REVERT: B  138 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7925 (mt-10)
REVERT: B  254 ASP cc_start: 0.7399 (t70) cc_final: 0.7097 (t70)
  outliers start: 22
  outliers final: 21
  residues processed: 126
  average time/residue: 0.0586
  time to fit residues: 10.7756
Evaluate side-chains
  124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  229 HIS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.170785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.131994 restraints weight = 7291.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 1.90
r_work: 0.3450 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7007  Z= 0.147
  Angle     :  0.541   8.408   9532  Z= 0.275
  Chirality :  0.041   0.168   1126
  Planarity :  0.003   0.047   1199
  Dihedral  :  4.644  76.007    963
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.81 %
    Favored  : 79.63 %
  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 are not related in a simple way.
  whole:  0.72 (0.29), residues: 894
  helix:  2.18 (0.26), residues: 399
  sheet: -0.70 (0.40), residues: 158
  loop : -1.01 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  52 
 TYR   0.010   0.001   TYR R 257 
 PHE   0.009   0.001   PHE A 274 
 TRP   0.031   0.002   TRP B 339 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7006)
  covalent geometry    : angle       0.54121 ( 9530)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.18933 (    2)
  hydrogen bonds       : bond        0.03451 (  388)
  hydrogen bonds       : angle       4.60661 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.260 
Fit side-chains
REVERT: R  152 MET cc_start: 0.6976 (tpt) cc_final: 0.6750 (tpt)
REVERT: R  229 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6703 (t-90)
REVERT: R  303 PHE cc_start: 0.7934 (m-10) cc_final: 0.7570 (m-10)
REVERT: B  138 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8046 (mt-10)
REVERT: B  254 ASP cc_start: 0.7378 (t70) cc_final: 0.7059 (t70)
  outliers start: 25
  outliers final: 23
  residues processed: 126
  average time/residue: 0.0667
  time to fit residues: 12.0548
Evaluate side-chains
  130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  229 HIS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 27 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 52 optimal weight:   20.0000
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.169317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129815 restraints weight = 7280.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.94
r_work: 0.3430 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7007  Z= 0.156
  Angle     :  0.552   8.485   9532  Z= 0.281
  Chirality :  0.041   0.155   1126
  Planarity :  0.003   0.046   1199
  Dihedral  :  4.690  76.065    963
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.95 %
    Favored  : 79.49 %
  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 are not related in a simple way.
  whole:  0.60 (0.29), residues: 894
  helix:  2.08 (0.26), residues: 398
  sheet: -0.82 (0.40), residues: 158
  loop : -1.03 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R  54 
 TYR   0.014   0.001   TYR A 296 
 PHE   0.009   0.001   PHE A 274 
 TRP   0.033   0.002   TRP B 339 
 HIS   0.002   0.001   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7006)
  covalent geometry    : angle       0.55183 ( 9530)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.15448 (    2)
  hydrogen bonds       : bond        0.03506 (  388)
  hydrogen bonds       : angle       4.68484 ( 1110)

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.260 
Fit side-chains
REVERT: R   54 ARG cc_start: 0.7268 (mmp80) cc_final: 0.6149 (mmt180)
REVERT: R  229 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6717 (t-90)
REVERT: R  303 PHE cc_start: 0.7970 (m-10) cc_final: 0.7606 (m-10)
REVERT: A   53 MET cc_start: 0.6411 (pmm) cc_final: 0.5973 (pmm)
REVERT: B  138 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8044 (mt-10)
REVERT: B  254 ASP cc_start: 0.7497 (t70) cc_final: 0.7204 (t70)
  outliers start: 25
  outliers final: 23
  residues processed: 125
  average time/residue: 0.0625
  time to fit residues: 11.5191
Evaluate side-chains
  132 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   69 VAL
Chi-restraints excluded: chain R residue   78 LEU
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  161 ILE
Chi-restraints excluded: chain R residue  200 VAL
Chi-restraints excluded: chain R residue  229 HIS
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  315 ASP
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  339 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 52 optimal weight:   20.0000
   chunk 79 optimal weight:    3.9990
   chunk 41 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.170420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.131091 restraints weight = 7219.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 1.93
r_work: 0.3439 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7007  Z= 0.142
  Angle     :  0.543   8.402   9532  Z= 0.276
  Chirality :  0.041   0.147   1126
  Planarity :  0.003   0.046   1199
  Dihedral  :  4.667  75.273    963
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.38 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.29), residues: 894
  helix:  2.08 (0.26), residues: 398
  sheet: -0.84 (0.40), residues: 158
  loop : -1.03 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R  54 
 TYR   0.014   0.001   TYR A 296 
 PHE   0.009   0.001   PHE A 274 
 TRP   0.031   0.002   TRP B 339 
 HIS   0.002   0.000   HIS B  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7006)
  covalent geometry    : angle       0.54295 ( 9530)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.12905 (    2)
  hydrogen bonds       : bond        0.03439 (  388)
  hydrogen bonds       : angle       4.65016 ( 1110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2066.56 seconds
wall clock time: 36 minutes 5.03 seconds (2165.03 seconds total)