Starting phenix.real_space_refine
on Wed Sep 17 07:59:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d61_46585/09_2025/9d61_46585.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d61_46585/09_2025/9d61_46585.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d61_46585/09_2025/9d61_46585.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d61_46585/09_2025/9d61_46585.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d61_46585/09_2025/9d61_46585.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d61_46585/09_2025/9d61_46585.cif"
  }
  resolution = 3.58
  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=   0.008 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4399      2.51       5
     N    1156      2.21       5
     O    1288      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6895
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2145
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 9, 'TRANS': 276}
          Unresolved non-hydrogen bonds: 143
          Unresolved non-hydrogen angles: 183
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 102
    Chain: "C"
      Number of atoms: 2569
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2569
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "D"
      Number of atoms: 395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 395
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1752
          Classifications: {'peptide': 223}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 2, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'JDC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.94, per 1000 atoms: 0.28
  Number of scatterers: 6895
  At special positions: 0
  Unit cell: (93.168, 93.168, 120.342, 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      52     16.00
     O    1288      8.00
     N    1156      7.00
     C    4399      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 210 " 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: 0.61
  Conformation dependent library (CDL) restraints added in 337.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1714

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      46.5% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 87
      removed outlier: 4.082A  pdb=" N   ILE A  61 " --> pdb=" O   ALA A  57 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ILE A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 110
      removed outlier: 3.607A  pdb=" N   ILE A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TYR A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   THR A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 122
    Processing helix  chain 'A' and resid 126 through 161
      removed outlier: 4.250A  pdb=" N   LEU A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   CYS A 131 " --> pdb=" O   GLY A 127 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   LYS A 132 " --> pdb=" O   ASP A 128 " (cutoff:3.500A)
      removed outlier: 4.991A  pdb=" N   ILE A 133 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ASP A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TYR A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 170
      removed outlier: 3.715A  pdb=" N   LEU A 167 " --> pdb=" O   PRO A 163 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   ASP A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 196
      removed outlier: 3.769A  pdb=" N   VAL A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 236
    Processing helix  chain 'A' and resid 236 through 256
      removed outlier: 3.952A  pdb=" N   SER A 255 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL A 256 " --> pdb=" O   ARG A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 300
      removed outlier: 3.644A  pdb=" N   CYS A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
      removed outlier: 3.615A  pdb=" N   LEU A 299 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   GLY A 300 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 333
      removed outlier: 4.431A  pdb=" N   SER A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
      Proline residue:  A 327  - end of helix
    Processing helix  chain 'A' and resid 335 through 342
    Processing helix  chain 'C' and resid 3 through 25
    Processing helix  chain 'C' and resid 30 through 35
    Processing helix  chain 'D' and resid 9 through 24
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.599A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 28
    Processing helix  chain 'B' and resid 28 through 33
      removed outlier: 4.153A  pdb=" N   ARG B  32 " --> pdb=" O   GLU B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 50
      removed outlier: 3.632A  pdb=" N   ILE B  49 " --> pdb=" O   GLY B  45 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL B  50 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 45 through 50'
    Processing helix  chain 'B' and resid 207 through 215
      removed outlier: 3.530A  pdb=" N   LYS B 210 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 5.091A  pdb=" N   HIS B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   CYS B 214 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
    Processing helix  chain 'B' and resid 256 through 260
      removed outlier: 4.079A  pdb=" N   THR B 260 " --> pdb=" O   LYS B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 281
      removed outlier: 3.787A  pdb=" N   PHE B 274 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLU B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   LYS B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS B 280 " --> pdb=" O   GLU B 276 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   SER B 281 " --> pdb=" O   LYS B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 309
    Processing helix  chain 'B' and resid 330 through 351
      removed outlier: 3.902A  pdb=" N   PHE B 334 " --> pdb=" O   LYS B 330 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201
      removed outlier: 3.679A  pdb=" N   GLY A 198 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LYS A 200 " --> pdb=" O   GLU A 209 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   GLU A 209 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 50
      removed outlier: 3.503A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.793A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU C  70 " --> pdb=" O   TRP C  82 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105
      removed outlier: 3.665A  pdb=" N   ALA C 104 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR C 124 " --> pdb=" O   VAL C 112 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 160
      removed outlier: 3.779A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192
      removed outlier: 6.707A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.773A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278
      removed outlier: 4.395A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 40
      removed outlier: 6.080A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   PHE B 267 " --> pdb=" O   ILE B 221 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   PHE B 223 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ASN B 269 " --> pdb=" O   PHE B 223 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL B 225 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ILE B 264 " --> pdb=" O   TYR B 320 " (cutoff:3.500A)
      removed outlier: 7.973A  pdb=" N   HIS B 322 " --> pdb=" O   ILE B 264 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   LEU B 266 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 189
      removed outlier: 3.550A  pdb=" N   THR B 187 " --> pdb=" O   MET B 198 " (cutoff:3.500A)

    350 hydrogen bonds defined for protein.
    1020 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.17

  Time building geometry restraints manager: 0.79 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: 2202
        1.34 -     1.46: 1422
        1.46 -     1.58: 3326
        1.58 -     1.70: 0
        1.70 -     1.82: 73
  Bond restraints: 7023
  Sorted by residual:
  bond pdb=" C   THR A 288 "
       pdb=" N   PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.020 1.19e-02 7.06e+03 2.76e+00
  bond pdb=" C   ILE A  58 "
       pdb=" N   PRO A  59 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 9.40e-03 1.13e+04 1.72e+00
  bond pdb=" CG1 ILE A 292 "
       pdb=" CD1 ILE A 292 "
    ideal  model  delta    sigma   weight residual
    1.513  1.465  0.048 3.90e-02 6.57e+02 1.49e+00
  bond pdb=" CA  GLU B  43 "
       pdb=" CB  GLU B  43 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.27e+00
  bond pdb=" N   LYS B 270 "
       pdb=" CA  LYS B 270 "
    ideal  model  delta    sigma   weight residual
    1.460  1.474 -0.014 1.42e-02 4.96e+03 1.02e+00
  ... (remaining 7018 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 9224
        1.69 -     3.38: 264
        3.38 -     5.08: 34
        5.08 -     6.77: 14
        6.77 -     8.46: 10
  Bond angle restraints: 9546
  Sorted by residual:
  angle pdb=" N   ILE C 270 "
        pdb=" CA  ILE C 270 "
        pdb=" C   ILE C 270 "
      ideal   model   delta    sigma   weight residual
     113.20  108.70    4.50 9.60e-01 1.09e+00 2.20e+01
  angle pdb=" N   ARG C  68 "
        pdb=" CA  ARG C  68 "
        pdb=" CB  ARG C  68 "
      ideal   model   delta    sigma   weight residual
     114.17  109.41    4.76 1.14e+00 7.69e-01 1.74e+01
  angle pdb=" C   GLY B  42 "
        pdb=" N   GLU B  43 "
        pdb=" CA  GLU B  43 "
      ideal   model   delta    sigma   weight residual
     121.54  128.04   -6.50 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" C   ASN B 269 "
        pdb=" N   LYS B 270 "
        pdb=" CA  LYS B 270 "
      ideal   model   delta    sigma   weight residual
     122.82  127.57   -4.75 1.42e+00 4.96e-01 1.12e+01
  angle pdb=" CA  GLU B  43 "
        pdb=" CB  GLU B  43 "
        pdb=" CG  GLU B  43 "
      ideal   model   delta    sigma   weight residual
     114.10  120.28   -6.18 2.00e+00 2.50e-01 9.54e+00
  ... (remaining 9541 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.52: 3944
       21.52 -    43.04: 238
       43.04 -    64.55: 15
       64.55 -    86.07: 3
       86.07 -   107.59: 1
  Dihedral angle restraints: 4201
    sinusoidal: 1563
      harmonic: 2638
  Sorted by residual:
  dihedral pdb=" CA  ILE D  28 "
           pdb=" C   ILE D  28 "
           pdb=" N   LYS D  29 "
           pdb=" CA  LYS D  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.16  -20.84     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  TRP C  82 "
           pdb=" C   TRP C  82 "
           pdb=" N   ASP C  83 "
           pdb=" CA  ASP C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.88   19.12     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" C3B JDC A 401 "
           pdb=" C2A JDC A 401 "
           pdb=" C3A JDC A 401 "
           pdb=" N2A JDC A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.91  -49.68  107.59     1      3.00e+01 1.11e-03 1.39e+01
  ... (remaining 4198 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 791
       0.046 -    0.092: 268
       0.092 -    0.139: 70
       0.139 -    0.185: 5
       0.185 -    0.231: 3
  Chirality restraints: 1137
  Sorted by residual:
  chirality pdb=" CB  ILE C 157 "
            pdb=" CA  ILE C 157 "
            pdb=" CG1 ILE C 157 "
            pdb=" CG2 ILE C 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CG  LEU B 348 "
            pdb=" CB  LEU B 348 "
            pdb=" CD1 LEU B 348 "
            pdb=" CD2 LEU B 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.89e-01
  chirality pdb=" CG  LEU A 309 "
            pdb=" CB  LEU A 309 "
            pdb=" CD1 LEU A 309 "
            pdb=" CD2 LEU A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.18 2.00e-01 2.50e+01 8.53e-01
  ... (remaining 1134 not shown)

  Planarity restraints: 1199
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 141 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.86e+00
        pdb=" CG  ASN A 141 "    0.038 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 141 "   -0.014 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 141 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C  68 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.67e+00
        pdb=" C   ARG C  68 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ARG C  68 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU C  69 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 124 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO A 125 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 125 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 125 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1196 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1490
        2.78 -     3.31: 6517
        3.31 -     3.84: 11800
        3.84 -     4.37: 13248
        4.37 -     4.90: 23144
  Nonbonded interactions: 56199
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 105 "
            pdb=" OG1 THR A 109 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   VAL A 284 "
            pdb=" OG1 THR A 288 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ALA A 317 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OH  TYR B 230 "
            pdb=" OG  SER B 281 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG1 THR C 184 "
            pdb=" OD2 ASP C 205 "
     model   vdw
     2.324 3.040
  ... (remaining 56194 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 group one per residue
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:             1.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.670
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6245
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   0.048   7024  Z= 0.178
  Angle     :  0.745   8.461   9548  Z= 0.403
  Chirality :  0.048   0.231   1137
  Planarity :  0.005   0.045   1199
  Dihedral  : 12.935 107.591   2484
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  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: -1.57 (0.27), residues: 893
  helix: -0.25 (0.25), residues: 372
  sheet: -0.90 (0.43), residues: 157
  loop : -1.87 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  27 
 TYR   0.018   0.002   TYR A 140 
 PHE   0.022   0.002   PHE C 278 
 TRP   0.013   0.002   TRP C 339 
 HIS   0.004   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7023)
  covalent geometry    : angle       0.74423 ( 9546)
  SS BOND              : bond        0.00170 (    1)
  SS BOND              : angle       2.02822 (    2)
  hydrogen bonds       : bond        0.17289 (  350)
  hydrogen bonds       : angle       6.65343 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.286 
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: A  124 TRP cc_start: 0.5448 (p-90) cc_final: 0.4781 (p-90)
REVERT: C   17 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8537 (tm-30)
REVERT: C   19 ARG cc_start: 0.8898 (mtm180) cc_final: 0.8553 (ptp-110)
REVERT: C   57 LYS cc_start: 0.6640 (ttmt) cc_final: 0.5980 (ttmm)
REVERT: C  246 ASP cc_start: 0.7556 (t0) cc_final: 0.7320 (t0)
REVERT: C  255 LEU cc_start: 0.7040 (mm) cc_final: 0.6526 (tp)
REVERT: B   17 LYS cc_start: 0.8543 (mtmt) cc_final: 0.7935 (mmmt)
REVERT: B   33 GLU cc_start: 0.6486 (tp30) cc_final: 0.6255 (tp30)
REVERT: B  243 MET cc_start: 0.7699 (tpp) cc_final: 0.6972 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1175
  time to fit residues: 31.3969
Evaluate side-chains
  138 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN
C 156 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 HIS
B 244 HIS
B 333 GLN
B 346 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.153063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.134369 restraints weight = 15200.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.137739 restraints weight = 9916.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.138979 restraints weight = 6625.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.139139 restraints weight = 5473.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.139819 restraints weight = 5392.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.4491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6412
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7024  Z= 0.182
  Angle     :  0.671  10.327   9548  Z= 0.349
  Chirality :  0.043   0.197   1137
  Planarity :  0.004   0.044   1199
  Dihedral  :  6.113 107.958   1002
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 11.57 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.98 (0.28), residues: 893
  helix:  0.64 (0.27), residues: 373
  sheet: -0.97 (0.42), residues: 160
  loop : -1.87 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 197 
 TYR   0.014   0.002   TYR B 290 
 PHE   0.020   0.002   PHE C 241 
 TRP   0.023   0.003   TRP C 339 
 HIS   0.005   0.001   HIS B 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 7023)
  covalent geometry    : angle       0.67061 ( 9546)
  SS BOND              : bond        0.01734 (    1)
  SS BOND              : angle       1.31429 (    2)
  hydrogen bonds       : bond        0.03879 (  350)
  hydrogen bonds       : angle       5.16642 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 TRP cc_start: 0.5763 (p-90) cc_final: 0.4755 (p-90)
REVERT: A  208 ILE cc_start: 0.8479 (pt) cc_final: 0.8250 (pt)
REVERT: C    6 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7724 (tp-100)
REVERT: C  214 ARG cc_start: 0.5102 (mmp-170) cc_final: 0.4841 (mmp-170)
REVERT: C  255 LEU cc_start: 0.6908 (mm) cc_final: 0.6598 (tp)
REVERT: D   21 MET cc_start: 0.7102 (tmm) cc_final: 0.6811 (tmm)
REVERT: B   10 LYS cc_start: 0.7582 (mmpt) cc_final: 0.7327 (mmtt)
REVERT: B   17 LYS cc_start: 0.8460 (mtmt) cc_final: 0.8030 (mmmt)
REVERT: B   22 ASN cc_start: 0.8198 (p0) cc_final: 0.7880 (t0)
REVERT: B  197 LYS cc_start: 0.7160 (mtmt) cc_final: 0.6663 (ttmm)
REVERT: B  225 VAL cc_start: 0.5975 (p) cc_final: 0.5302 (p)
REVERT: B  247 MET cc_start: 0.6816 (mtt) cc_final: 0.6510 (ptp)
REVERT: B  314 LYS cc_start: 0.6460 (mmmt) cc_final: 0.6222 (mmtm)
  outliers start: 24
  outliers final: 15
  residues processed: 159
  average time/residue: 0.1101
  time to fit residues: 22.4255
Evaluate side-chains
  147 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain B residue   13 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 82 optimal weight:    0.0570
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 51 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 268 ASN
C 156 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.144284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.125032 restraints weight = 14868.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.125587 restraints weight = 10640.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.128116 restraints weight = 8532.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.128691 restraints weight = 6071.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.129459 restraints weight = 6055.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6456
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7024  Z= 0.136
  Angle     :  0.615   7.895   9548  Z= 0.319
  Chirality :  0.041   0.158   1137
  Planarity :  0.004   0.043   1199
  Dihedral  :  6.039 106.946   1002
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 15.98 %
    Favored  : 81.68 %
  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: -0.77 (0.28), residues: 893
  helix:  0.96 (0.28), residues: 368
  sheet: -0.92 (0.42), residues: 150
  loop : -1.84 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 197 
 TYR   0.032   0.002   TYR A  66 
 PHE   0.014   0.001   PHE C 241 
 TRP   0.014   0.002   TRP C 339 
 HIS   0.004   0.001   HIS C 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7023)
  covalent geometry    : angle       0.61443 ( 9546)
  SS BOND              : bond        0.00393 (    1)
  SS BOND              : angle       0.92628 (    2)
  hydrogen bonds       : bond        0.03399 (  350)
  hydrogen bonds       : angle       4.92885 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.274 
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: A  105 ASP cc_start: 0.6534 (OUTLIER) cc_final: 0.5895 (t0)
REVERT: A  208 ILE cc_start: 0.8381 (pt) cc_final: 0.7923 (pt)
REVERT: C  214 ARG cc_start: 0.5193 (mmp-170) cc_final: 0.4917 (mmp-170)
REVERT: C  255 LEU cc_start: 0.6963 (mm) cc_final: 0.6655 (tp)
REVERT: D   15 LEU cc_start: 0.8596 (pp) cc_final: 0.8393 (pp)
REVERT: D   17 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8081 (mm-30)
REVERT: D   32 LYS cc_start: 0.8393 (tmtt) cc_final: 0.7981 (tmmt)
REVERT: B   10 LYS cc_start: 0.7634 (mmpt) cc_final: 0.7364 (mmtt)
REVERT: B   22 ASN cc_start: 0.8301 (p0) cc_final: 0.7989 (t0)
REVERT: B  247 MET cc_start: 0.6953 (mtt) cc_final: 0.6591 (ptp)
  outliers start: 17
  outliers final: 14
  residues processed: 155
  average time/residue: 0.1090
  time to fit residues: 21.5901
Evaluate side-chains
  143 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   29 LYS
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0980
   chunk 82 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 87 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 268 ASN
C 156 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN
B 204 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.142928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.122710 restraints weight = 15079.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.124911 restraints weight = 10115.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.127141 restraints weight = 7925.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.127958 restraints weight = 5768.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.128014 restraints weight = 5392.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6490
moved from start:          0.3753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7024  Z= 0.141
  Angle     :  0.599   7.522   9548  Z= 0.312
  Chirality :  0.041   0.171   1137
  Planarity :  0.003   0.048   1199
  Dihedral  :  5.932 104.373   1002
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.46 %
    Favored  : 78.37 %
  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: -0.52 (0.29), residues: 893
  helix:  1.19 (0.28), residues: 368
  sheet: -0.73 (0.43), residues: 146
  loop : -1.76 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 197 
 TYR   0.019   0.002   TYR A  66 
 PHE   0.016   0.002   PHE C 241 
 TRP   0.015   0.002   TRP A 124 
 HIS   0.003   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7023)
  covalent geometry    : angle       0.59932 ( 9546)
  SS BOND              : bond        0.00341 (    1)
  SS BOND              : angle       1.07895 (    2)
  hydrogen bonds       : bond        0.03218 (  350)
  hydrogen bonds       : angle       4.75706 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.5658 (t0)
REVERT: A  208 ILE cc_start: 0.8395 (pt) cc_final: 0.8159 (pt)
REVERT: C  188 MET cc_start: 0.7631 (ptp) cc_final: 0.7164 (mtm)
REVERT: C  214 ARG cc_start: 0.5244 (mmp-170) cc_final: 0.5029 (mmp-170)
REVERT: C  255 LEU cc_start: 0.7073 (mm) cc_final: 0.6782 (tp)
REVERT: D   17 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: B  247 MET cc_start: 0.7035 (mtt) cc_final: 0.6666 (ptp)
REVERT: B  276 GLU cc_start: 0.7185 (pm20) cc_final: 0.6404 (pm20)
  outliers start: 23
  outliers final: 13
  residues processed: 149
  average time/residue: 0.1056
  time to fit residues: 20.3239
Evaluate side-chains
  142 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   29 LYS
Chi-restraints excluded: chain B residue   17 LYS
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0970
   chunk 68 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 48 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 15 optimal weight:    7.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 268 ASN
C  13 GLN
C 156 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.141919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.121822 restraints weight = 15035.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.124089 restraints weight = 9748.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.124776 restraints weight = 8448.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.125904 restraints weight = 6440.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.126368 restraints weight = 5652.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6530
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7024  Z= 0.141
  Angle     :  0.621   8.760   9548  Z= 0.321
  Chirality :  0.042   0.182   1137
  Planarity :  0.004   0.045   1199
  Dihedral  :  5.926 105.255   1002
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 21.21 %
    Favored  : 75.34 %
  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: -0.54 (0.28), residues: 893
  helix:  1.20 (0.28), residues: 367
  sheet: -0.91 (0.43), residues: 150
  loop : -1.71 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 197 
 TYR   0.017   0.001   TYR A  66 
 PHE   0.016   0.002   PHE C 241 
 TRP   0.013   0.002   TRP B 211 
 HIS   0.003   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7023)
  covalent geometry    : angle       0.62038 ( 9546)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       1.40031 (    2)
  hydrogen bonds       : bond        0.03212 (  350)
  hydrogen bonds       : angle       4.72381 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6767 (mt)
REVERT: A  105 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6372 (t70)
REVERT: C  114 CYS cc_start: 0.6569 (t) cc_final: 0.6169 (t)
REVERT: C  233 CYS cc_start: 0.5629 (p) cc_final: 0.5393 (p)
REVERT: C  255 LEU cc_start: 0.7109 (mm) cc_final: 0.6779 (tp)
REVERT: D   15 LEU cc_start: 0.8648 (pp) cc_final: 0.8310 (pp)
REVERT: D   17 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8133 (mm-30)
REVERT: D   32 LYS cc_start: 0.8661 (ptpt) cc_final: 0.8418 (tmtt)
REVERT: B   20 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.7037 (m-30)
REVERT: B  277 LYS cc_start: 0.7113 (mmtt) cc_final: 0.6755 (mmtt)
  outliers start: 25
  outliers final: 16
  residues processed: 155
  average time/residue: 0.1023
  time to fit residues: 20.5782
Evaluate side-chains
  147 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  183 HIS
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain B residue   20 ASP
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 83 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0980
   chunk 62 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 268 ASN
C   6 GLN
C 156 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.141320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.121820 restraints weight = 15221.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.123582 restraints weight = 9898.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.124787 restraints weight = 8346.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.125363 restraints weight = 5982.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.126914 restraints weight = 5610.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7024  Z= 0.146
  Angle     :  0.642   9.304   9548  Z= 0.334
  Chirality :  0.042   0.185   1137
  Planarity :  0.003   0.040   1199
  Dihedral  :  6.002 105.385   1002
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 21.90 %
    Favored  : 73.69 %
  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: -0.39 (0.29), residues: 893
  helix:  1.38 (0.28), residues: 360
  sheet: -0.77 (0.44), residues: 149
  loop : -1.66 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.021   0.001   TYR A 246 
 PHE   0.034   0.002   PHE A 293 
 TRP   0.022   0.002   TRP A 124 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7023)
  covalent geometry    : angle       0.64166 ( 9546)
  SS BOND              : bond        0.00663 (    1)
  SS BOND              : angle       1.11060 (    2)
  hydrogen bonds       : bond        0.03230 (  350)
  hydrogen bonds       : angle       4.75786 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6742 (mt)
REVERT: A  105 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6445 (t70)
REVERT: A  235 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6530 (m-10)
REVERT: C  255 LEU cc_start: 0.7156 (mm) cc_final: 0.6831 (tp)
REVERT: D   15 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8340 (pp)
REVERT: D   17 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8209 (mm-30)
REVERT: B   22 ASN cc_start: 0.8283 (p0) cc_final: 0.7856 (t0)
REVERT: B  247 MET cc_start: 0.7014 (mtt) cc_final: 0.6647 (ptp)
  outliers start: 32
  outliers final: 20
  residues processed: 156
  average time/residue: 0.1034
  time to fit residues: 21.0263
Evaluate side-chains
  148 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain C residue    6 GLN
Chi-restraints excluded: chain C residue   47 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  183 HIS
Chi-restraints excluded: chain C residue  276 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 268 ASN
C   6 GLN
C  13 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.140099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.120438 restraints weight = 15006.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.122309 restraints weight = 9709.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.122608 restraints weight = 9173.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.123708 restraints weight = 6811.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.123984 restraints weight = 6176.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6603
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7024  Z= 0.168
  Angle     :  0.679  10.189   9548  Z= 0.351
  Chirality :  0.043   0.192   1137
  Planarity :  0.004   0.043   1199
  Dihedral  :  6.026 105.725   1002
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 22.73 %
    Favored  : 73.28 %
  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: -0.52 (0.29), residues: 893
  helix:  1.25 (0.28), residues: 361
  sheet: -1.03 (0.43), residues: 157
  loop : -1.63 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.019   0.002   TYR A 246 
 PHE   0.027   0.002   PHE A 293 
 TRP   0.016   0.002   TRP B 211 
 HIS   0.003   0.001   HIS D  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 7023)
  covalent geometry    : angle       0.67891 ( 9546)
  SS BOND              : bond        0.00469 (    1)
  SS BOND              : angle       1.40698 (    2)
  hydrogen bonds       : bond        0.03270 (  350)
  hydrogen bonds       : angle       4.74975 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6824 (mt)
REVERT: A  105 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6561 (t70)
REVERT: A  235 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6477 (m-10)
REVERT: C   57 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5795 (ttpp)
REVERT: C  114 CYS cc_start: 0.6118 (t) cc_final: 0.5818 (t)
REVERT: C  255 LEU cc_start: 0.7165 (mm) cc_final: 0.6860 (tp)
REVERT: D   15 LEU cc_start: 0.8647 (pp) cc_final: 0.8327 (pp)
REVERT: D   17 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8217 (mm-30)
REVERT: B   22 ASN cc_start: 0.8386 (p0) cc_final: 0.7952 (t0)
REVERT: B  192 LYS cc_start: 0.7283 (mttm) cc_final: 0.7061 (mttm)
REVERT: B  247 MET cc_start: 0.7104 (mtt) cc_final: 0.6727 (ptp)
REVERT: B  276 GLU cc_start: 0.6833 (pm20) cc_final: 0.6516 (pm20)
REVERT: B  277 LYS cc_start: 0.7380 (mmtt) cc_final: 0.6918 (mmtt)
  outliers start: 29
  outliers final: 22
  residues processed: 149
  average time/residue: 0.1067
  time to fit residues: 20.4758
Evaluate side-chains
  148 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  168 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain C residue    6 GLN
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  183 HIS
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  340 ASN
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 83 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 85 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 268 ASN
C 156 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 322 HIS ** 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 = 0.4432 r_free = 0.4432 target = 0.139950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.120369 restraints weight = 15229.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.122026 restraints weight = 9772.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.122953 restraints weight = 8831.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.123799 restraints weight = 6450.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.125052 restraints weight = 5867.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6582
moved from start:          0.4794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7024  Z= 0.162
  Angle     :  0.679  10.452   9548  Z= 0.353
  Chirality :  0.042   0.196   1137
  Planarity :  0.003   0.042   1199
  Dihedral  :  6.044 105.998   1002
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.10 %
    Favored  : 71.90 %
  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 aren not related in a simple way.
  whole: -0.50 (0.29), residues: 893
  helix:  1.16 (0.28), residues: 366
  sheet: -0.90 (0.44), residues: 155
  loop : -1.60 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 270 
 TYR   0.017   0.002   TYR A 246 
 PHE   0.021   0.002   PHE A 293 
 TRP   0.014   0.002   TRP B 211 
 HIS   0.003   0.001   HIS B 322 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 7023)
  covalent geometry    : angle       0.67861 ( 9546)
  SS BOND              : bond        0.00385 (    1)
  SS BOND              : angle       1.23636 (    2)
  hydrogen bonds       : bond        0.03317 (  350)
  hydrogen bonds       : angle       4.76593 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6731 (mt)
REVERT: A  105 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6533 (t70)
REVERT: A  235 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.6418 (m-10)
REVERT: A  292 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5435 (mp)
REVERT: A  329 LEU cc_start: 0.7907 (tp) cc_final: 0.7580 (tt)
REVERT: C   57 LYS cc_start: 0.6384 (ttpp) cc_final: 0.6083 (ttpp)
REVERT: C  114 CYS cc_start: 0.6129 (t) cc_final: 0.5866 (t)
REVERT: C  255 LEU cc_start: 0.7191 (mm) cc_final: 0.6887 (tp)
REVERT: C  270 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7994 (tp)
REVERT: D   17 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8232 (mm-30)
REVERT: B   22 ASN cc_start: 0.8365 (p0) cc_final: 0.7950 (t0)
REVERT: B  192 LYS cc_start: 0.7326 (mttm) cc_final: 0.7008 (mttm)
REVERT: B  247 MET cc_start: 0.6993 (mtt) cc_final: 0.6680 (ptp)
REVERT: B  276 GLU cc_start: 0.6720 (pm20) cc_final: 0.6138 (pm20)
REVERT: B  277 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6946 (mmtt)
  outliers start: 29
  outliers final: 19
  residues processed: 147
  average time/residue: 0.1096
  time to fit residues: 20.6010
Evaluate side-chains
  146 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  183 HIS
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  257 LYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 87 optimal weight:    0.0770
   chunk 41 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0870
   chunk 22 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 268 ASN
C  13 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 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 = 0.4450 r_free = 0.4450 target = 0.141239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.121350 restraints weight = 15127.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.122798 restraints weight = 9811.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.123604 restraints weight = 9229.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.124537 restraints weight = 6733.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.126369 restraints weight = 6009.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6558
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7024  Z= 0.143
  Angle     :  0.687  11.590   9548  Z= 0.357
  Chirality :  0.042   0.252   1137
  Planarity :  0.003   0.041   1199
  Dihedral  :  6.039 105.599   1002
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 25.62 %
    Favored  : 71.35 %
  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: -0.56 (0.29), residues: 893
  helix:  1.14 (0.28), residues: 365
  sheet: -1.09 (0.43), residues: 164
  loop : -1.57 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 252 
 TYR   0.016   0.001   TYR A 246 
 PHE   0.017   0.001   PHE A 293 
 TRP   0.015   0.002   TRP B 258 
 HIS   0.002   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7023)
  covalent geometry    : angle       0.68697 ( 9546)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       1.15114 (    2)
  hydrogen bonds       : bond        0.03288 (  350)
  hydrogen bonds       : angle       4.71033 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6682 (mt)
REVERT: A  105 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6449 (t70)
REVERT: A  235 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.6305 (m-10)
REVERT: A  329 LEU cc_start: 0.7909 (tp) cc_final: 0.7587 (tt)
REVERT: A  335 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.6005 (pm20)
REVERT: C   57 LYS cc_start: 0.6203 (ttpp) cc_final: 0.5926 (ttpp)
REVERT: C  114 CYS cc_start: 0.5733 (t) cc_final: 0.5354 (t)
REVERT: C  255 LEU cc_start: 0.7197 (mm) cc_final: 0.6901 (tp)
REVERT: D   17 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8249 (mm-30)
REVERT: B   22 ASN cc_start: 0.8364 (p0) cc_final: 0.7938 (t0)
REVERT: B   36 LEU cc_start: 0.8347 (mt) cc_final: 0.8032 (mt)
REVERT: B  247 MET cc_start: 0.7049 (mtt) cc_final: 0.6714 (ptp)
REVERT: B  276 GLU cc_start: 0.6805 (pm20) cc_final: 0.6422 (pm20)
REVERT: B  277 LYS cc_start: 0.7347 (mmtt) cc_final: 0.7017 (mmtt)
  outliers start: 22
  outliers final: 16
  residues processed: 147
  average time/residue: 0.1081
  time to fit residues: 20.3631
Evaluate side-chains
  143 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  179 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 82 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 268 ASN
C  88 ASN
C 156 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 340 ASN
** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.150755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.133177 restraints weight = 15232.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.135023 restraints weight = 11177.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.136963 restraints weight = 8474.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.137098 restraints weight = 6646.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.137243 restraints weight = 6111.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.4426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7024  Z= 0.174
  Angle     :  0.725  11.098   9548  Z= 0.375
  Chirality :  0.043   0.239   1137
  Planarity :  0.004   0.042   1199
  Dihedral  :  6.140 105.777   1002
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 25.62 %
    Favored  : 71.21 %
  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: -0.65 (0.29), residues: 893
  helix:  1.01 (0.27), residues: 365
  sheet: -1.02 (0.43), residues: 159
  loop : -1.61 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 252 
 TYR   0.017   0.002   TYR A 246 
 PHE   0.016   0.002   PHE C 278 
 TRP   0.042   0.003   TRP C 339 
 HIS   0.003   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 7023)
  covalent geometry    : angle       0.72507 ( 9546)
  SS BOND              : bond        0.00355 (    1)
  SS BOND              : angle       1.17983 (    2)
  hydrogen bonds       : bond        0.03390 (  350)
  hydrogen bonds       : angle       4.81507 ( 1020)

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6725 (mt)
REVERT: A  105 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6688 (t70)
REVERT: A  235 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.6272 (m-10)
REVERT: A  329 LEU cc_start: 0.8054 (tp) cc_final: 0.7744 (tt)
REVERT: A  335 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5795 (pm20)
REVERT: C   57 LYS cc_start: 0.5936 (ttpp) cc_final: 0.5673 (ttmm)
REVERT: C  114 CYS cc_start: 0.5722 (t) cc_final: 0.5310 (t)
REVERT: C  255 LEU cc_start: 0.7047 (mm) cc_final: 0.6811 (tp)
REVERT: D   17 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8142 (mm-30)
REVERT: B   22 ASN cc_start: 0.8203 (p0) cc_final: 0.7855 (t0)
REVERT: B  247 MET cc_start: 0.6965 (mtt) cc_final: 0.6675 (ptp)
  outliers start: 23
  outliers final: 17
  residues processed: 142
  average time/residue: 0.1080
  time to fit residues: 19.8105
Evaluate side-chains
  143 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  105 ASP
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  235 PHE
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  335 GLU
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  183 HIS
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain C residue  340 ASN
Chi-restraints excluded: chain D residue   15 LEU
Chi-restraints excluded: chain B residue   35 LYS
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  254 CYS
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 49 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0570
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
A 179 ASN
A 268 ASN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.150811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.132133 restraints weight = 15200.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.134042 restraints weight = 10273.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.134923 restraints weight = 9040.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.135551 restraints weight = 7024.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.136006 restraints weight = 6271.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.5189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7024  Z= 0.153
  Angle     :  0.725  11.908   9548  Z= 0.372
  Chirality :  0.043   0.219   1137
  Planarity :  0.003   0.041   1199
  Dihedral  :  6.090 105.099   1002
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 25.90 %
    Favored  : 71.07 %
  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: -0.66 (0.29), residues: 893
  helix:  0.95 (0.27), residues: 371
  sheet: -0.92 (0.43), residues: 159
  loop : -1.67 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 252 
 TYR   0.020   0.001   TYR C  59 
 PHE   0.013   0.001   PHE C 278 
 TRP   0.034   0.002   TRP C 339 
 HIS   0.002   0.001   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7023)
  covalent geometry    : angle       0.72525 ( 9546)
  SS BOND              : bond        0.00261 (    1)
  SS BOND              : angle       1.03588 (    2)
  hydrogen bonds       : bond        0.03362 (  350)
  hydrogen bonds       : angle       4.75527 ( 1020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1408.76 seconds
wall clock time: 25 minutes 15.66 seconds (1515.66 seconds total)