Starting phenix.real_space_refine
on Wed Feb  4 06:28:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vi9_65081/02_2026/9vi9_65081.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vi9_65081/02_2026/9vi9_65081.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vi9_65081/02_2026/9vi9_65081.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vi9_65081/02_2026/9vi9_65081.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vi9_65081/02_2026/9vi9_65081.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vi9_65081/02_2026/9vi9_65081.map"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 sd=   1.056
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      68      5.16       5
     C    5746      2.51       5
     N    1547      2.21       5
     O    1664      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9025
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2394
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1754
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "D"
      Number of atoms: 413
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 413
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "P"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 69
          Classifications: {'peptide': 9}
          Link IDs: {'PTRANS': 2, 'TRANS': 6}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "S"
      Number of atoms: 1794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1794
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 10, 'TRANS': 222}
          Chain breaks: 1
  Time building chain proxies: 2.29, per 1000 atoms: 0.25
  Number of scatterers: 9025
  At special positions: 0
  Unit cell: (96, 122.88, 138.24, 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      68     16.00
     O    1664      8.00
     N    1547      7.00
     C    5746      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 116 " - pdb=" SG  CYS A 203 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 356.2 milliseconds
  

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 14 sheets defined
      35.2% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 71
      removed outlier: 3.725A  pdb=" N   ASN A  71 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 106
      removed outlier: 3.830A  pdb=" N   MET A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      Proline residue:  A  98  - end of helix
    Processing helix  chain 'A' and resid 112 through 147
      removed outlier: 3.930A  pdb=" N   HIS A 147 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 179
      removed outlier: 3.616A  pdb=" N   ALA A 158 " --> pdb=" O   THR A 154 " (cutoff:3.500A)
      Proline residue:  A 175  - end of helix
    Processing helix  chain 'A' and resid 209 through 211
      No H-bonds generated for 'chain 'A' and resid 209 through 211'
    Processing helix  chain 'A' and resid 212 through 225
    Processing helix  chain 'A' and resid 225 through 246
      removed outlier: 3.723A  pdb=" N   LEU A 229 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 246 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 296
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 299 through 331
      removed outlier: 5.512A  pdb=" N   PHE A 311 " --> pdb=" O   THR A 307 " (cutoff:3.500A)
      Proline residue:  A 312  - end of helix
      removed outlier: 3.784A  pdb=" N   SER A 322 " --> pdb=" O   ALA A 318 " (cutoff:3.500A)
      Proline residue:  A 326  - end of helix
    Processing helix  chain 'B' and resid 7 through 31
    Processing helix  chain 'B' and resid 45 through 54
      removed outlier: 4.023A  pdb=" N   VAL B  50 " --> pdb=" O   LYS B  46 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LYS B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 3.737A  pdb=" N   ILE B 212 " --> pdb=" O   LYS B 209 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   HIS B 213 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   CYS B 214 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   PHE B 215 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
    Processing helix  chain 'B' and resid 273 through 281
    Processing helix  chain 'B' and resid 295 through 310
      removed outlier: 3.976A  pdb=" N   LEU B 310 " --> pdb=" O   GLN B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 351
      removed outlier: 3.989A  pdb=" N   CYS B 351 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 24
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 280 through 282
      No H-bonds generated for 'chain 'C' and resid 280 through 282'
    Processing helix  chain 'D' and resid 40 through 52
      removed outlier: 3.838A  pdb=" N   MET D  52 " --> pdb=" O   GLU D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 56
    Processing helix  chain 'D' and resid 60 through 70
      removed outlier: 4.171A  pdb=" N   ALA D  64 " --> pdb=" O   LYS D  60 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA D  70 " --> pdb=" O   ALA D  66 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34
      removed outlier: 5.930A  pdb=" N   THR A  31 " --> pdb=" O   PHE A 189 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   VAL A 191 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   SER A  33 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 184
    Processing sheet with id=AA3, first strand: chain 'B' and resid 185 through 190
      removed outlier: 3.898A  pdb=" N   ALA B 220 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   HIS B 322 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU B 268 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 51
      removed outlier: 4.159A  pdb=" N   ARG C  46 " --> pdb=" O   ASN C 340 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 5.722A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.955A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   HIS C  91 " --> pdb=" O   ILE C  81 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.967A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.028A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 153
      removed outlier: 6.869A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.468A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.898A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 232
      removed outlier: 6.821A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.598A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7
    Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 5.067A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 159
    Processing sheet with id=AB5, first strand: chain 'S' and resid 186 through 189
      removed outlier: 5.784A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1203 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: 1.62

  Time building geometry restraints manager: 0.96 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: 2910
        1.34 -     1.47: 2300
        1.47 -     1.59: 3909
        1.59 -     1.72: 0
        1.72 -     1.84: 102
  Bond restraints: 9221
  Sorted by residual:
  bond pdb=" C   PHE P   8 "
       pdb=" N   ALA P   9 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.40e-02 5.10e+03 2.83e+00
  bond pdb=" CG  LEU C  51 "
       pdb=" CD1 LEU C  51 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.82e+00
  bond pdb=" CB  ASP B 200 "
       pdb=" CG  ASP B 200 "
    ideal  model  delta    sigma   weight residual
    1.516  1.550 -0.034 2.50e-02 1.60e+03 1.80e+00
  bond pdb=" CB  MET A 235 "
       pdb=" CG  MET A 235 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.78e+00
  bond pdb=" CB  LYS B  29 "
       pdb=" CG  LYS B  29 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.66e+00
  ... (remaining 9216 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 12259
        2.32 -     4.64: 186
        4.64 -     6.96: 32
        6.96 -     9.28: 10
        9.28 -    11.61: 6
  Bond angle restraints: 12493
  Sorted by residual:
  angle pdb=" CA  MET A  45 "
        pdb=" CB  MET A  45 "
        pdb=" CG  MET A  45 "
      ideal   model   delta    sigma   weight residual
     114.10  123.46   -9.36 2.00e+00 2.50e-01 2.19e+01
  angle pdb=" CA  LYS B  29 "
        pdb=" CB  LYS B  29 "
        pdb=" CG  LYS B  29 "
      ideal   model   delta    sigma   weight residual
     114.10  121.25   -7.15 2.00e+00 2.50e-01 1.28e+01
  angle pdb=" CB  MET C 325 "
        pdb=" CG  MET C 325 "
        pdb=" SD  MET C 325 "
      ideal   model   delta    sigma   weight residual
     112.70  123.09  -10.39 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" CA  MET S  93 "
        pdb=" CB  MET S  93 "
        pdb=" CG  MET S  93 "
      ideal   model   delta    sigma   weight residual
     114.10  121.00   -6.90 2.00e+00 2.50e-01 1.19e+01
  angle pdb=" CB  MET A  45 "
        pdb=" CG  MET A  45 "
        pdb=" SD  MET A  45 "
      ideal   model   delta    sigma   weight residual
     112.70  122.93  -10.23 3.00e+00 1.11e-01 1.16e+01
  ... (remaining 12488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4686
       17.99 -    35.99: 601
       35.99 -    53.98: 143
       53.98 -    71.97: 31
       71.97 -    89.97: 9
  Dihedral angle restraints: 5470
    sinusoidal: 2131
      harmonic: 3339
  Sorted by residual:
  dihedral pdb=" CA  LEU B 268 "
           pdb=" C   LEU B 268 "
           pdb=" N   ASN B 269 "
           pdb=" CA  ASN B 269 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.56  -22.44     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  LEU C  51 "
           pdb=" C   LEU C  51 "
           pdb=" N   ARG C  52 "
           pdb=" CA  ARG C  52 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.38  -20.62     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ASP C 170 "
           pdb=" C   ASP C 170 "
           pdb=" N   ILE C 171 "
           pdb=" CA  ILE C 171 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.25  -18.75     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 5467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 974
       0.040 -    0.080: 313
       0.080 -    0.120: 109
       0.120 -    0.160: 15
       0.160 -    0.201: 3
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CG  LEU C 284 "
            pdb=" CB  LEU C 284 "
            pdb=" CD1 LEU C 284 "
            pdb=" CD2 LEU C 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CG  LEU D  46 "
            pdb=" CB  LEU D  46 "
            pdb=" CD1 LEU D  46 "
            pdb=" CD2 LEU D  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.18 2.00e-01 2.50e+01 8.56e-01
  chirality pdb=" CA  ILE C  93 "
            pdb=" N   ILE C  93 "
            pdb=" C   ILE C  93 "
            pdb=" CB  ILE C  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.05e-01
  ... (remaining 1411 not shown)

  Planarity restraints: 1577
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 297 "    0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   GLN A 297 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   GLN A 297 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LEU A 298 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 235 "    0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO S 236 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO S 236 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO S 236 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 306 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.96e+00
        pdb=" C   VAL A 306 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL A 306 "    0.011 2.00e-02 2.50e+03
        pdb=" N   THR A 307 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1574 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     2.99: 4576
        2.99 -     3.47: 8893
        3.47 -     3.95: 13518
        3.95 -     4.42: 15135
        4.42 -     4.90: 25649
  Nonbonded interactions: 67771
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 125 "
            pdb=" OD1 ASN C 125 "
     model   vdw
     2.516 3.040
  nonbonded pdb=" OD1 ASN C 119 "
            pdb=" O   GLY C 144 "
     model   vdw
     2.524 3.040
  nonbonded pdb=" O   ASP C 154 "
            pdb=" OD1 ASP C 154 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" N   ASP C  76 "
            pdb=" OD1 ASP C  76 "
     model   vdw
     2.555 3.120
  nonbonded pdb=" OD1 ASN A  84 "
            pdb=" OG1 THR A 133 "
     model   vdw
     2.603 3.040
  ... (remaining 67766 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.460
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.290
  Find NCS groups from input model:        0.050
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9222  Z= 0.167
  Angle     :  0.776  11.606  12495  Z= 0.398
  Chirality :  0.045   0.201   1414
  Planarity :  0.004   0.047   1577
  Dihedral  : 17.169  89.967   3307
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 31.30 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.25), residues: 1128
  helix:  1.78 (0.28), residues: 373
  sheet:  0.43 (0.31), residues: 283
  loop : -1.22 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 267 
 TYR   0.015   0.002   TYR B 320 
 PHE   0.015   0.001   PHE A  46 
 TRP   0.017   0.002   TRP C  63 
 HIS   0.009   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9221)
  covalent geometry    : angle       0.77446 (12493)
  SS BOND              : bond        0.00643 (    1)
  SS BOND              : angle       4.19955 (    2)
  hydrogen bonds       : bond        0.12072 (  420)
  hydrogen bonds       : angle       5.06004 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   45 MET cc_start: 0.4969 (ppp) cc_final: 0.4596 (ppp)
REVERT: A   80 MET cc_start: 0.6029 (ppp) cc_final: 0.5702 (ppp)
REVERT: A  190 MET cc_start: 0.2537 (ptm) cc_final: 0.2081 (ptm)
REVERT: B   14 GLU cc_start: 0.6667 (tm-30) cc_final: 0.6440 (tt0)
REVERT: B   17 LYS cc_start: 0.6201 (mmtp) cc_final: 0.5997 (mmtp)
REVERT: B   20 ASP cc_start: 0.7206 (m-30) cc_final: 0.6544 (m-30)
REVERT: B   32 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7613 (ttp-110)
REVERT: B  200 ASP cc_start: 0.7989 (t0) cc_final: 0.7687 (t70)
REVERT: B  260 THR cc_start: 0.8112 (m) cc_final: 0.7793 (m)
REVERT: C   65 THR cc_start: 0.7580 (m) cc_final: 0.7361 (m)
REVERT: C  118 ASP cc_start: 0.7330 (p0) cc_final: 0.7046 (p0)
REVERT: C  175 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7823 (mm-40)
REVERT: C  259 GLN cc_start: 0.7165 (pm20) cc_final: 0.6904 (pm20)
REVERT: D   77 LYS cc_start: 0.3638 (OUTLIER) cc_final: 0.2985 (tptt)
REVERT: P    3 ASN cc_start: 0.6285 (p0) cc_final: 0.5951 (p0)
REVERT: S   52 SER cc_start: 0.4752 (t) cc_final: 0.4192 (t)
  outliers start: 13
  outliers final: 10
  residues processed: 182
  average time/residue: 0.1064
  time to fit residues: 26.5526
Evaluate side-chains
  182 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 171
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain B residue  261 ASP
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain D residue   69 MET
Chi-restraints excluded: chain D residue   77 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   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  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
B 188 HIS
** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 142 HIS
D  90 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.202386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.164974 restraints weight = 14726.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4070 rms_B_bonded: 3.09
r_work: 0.3884 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6862
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9222  Z= 0.160
  Angle     :  0.651  10.291  12495  Z= 0.330
  Chirality :  0.044   0.158   1414
  Planarity :  0.004   0.044   1577
  Dihedral  :  5.383  58.037   1264
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 25.41 %
    Favored  : 69.21 %
  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 are not related in a simple way.
  whole:  0.23 (0.25), residues: 1128
  helix:  1.85 (0.26), residues: 372
  sheet:  0.43 (0.31), residues: 277
  loop : -1.42 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 184 
 TYR   0.016   0.001   TYR S 190 
 PHE   0.015   0.002   PHE S  27 
 TRP   0.016   0.002   TRP C  63 
 HIS   0.003   0.001   HIS C 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9221)
  covalent geometry    : angle       0.64904 (12493)
  SS BOND              : bond        0.00723 (    1)
  SS BOND              : angle       3.76654 (    2)
  hydrogen bonds       : bond        0.05331 (  420)
  hydrogen bonds       : angle       4.28224 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 187
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.6022 (ppp) cc_final: 0.5648 (ppp)
REVERT: A  112 ASP cc_start: 0.5660 (p0) cc_final: 0.5268 (p0)
REVERT: A  170 LEU cc_start: 0.7580 (tm) cc_final: 0.7306 (tt)
REVERT: A  205 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5874 (mt-10)
REVERT: A  307 THR cc_start: 0.8585 (p) cc_final: 0.8380 (t)
REVERT: A  320 PHE cc_start: 0.8240 (t80) cc_final: 0.7875 (t80)
REVERT: A  332 PHE cc_start: 0.7212 (m-10) cc_final: 0.6934 (m-10)
REVERT: B   18 MET cc_start: 0.7603 (ttm) cc_final: 0.7375 (ttt)
REVERT: B   20 ASP cc_start: 0.7256 (m-30) cc_final: 0.6751 (m-30)
REVERT: B   23 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6793 (mt)
REVERT: B  209 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7690 (ttpt)
REVERT: B  240 MET cc_start: 0.3983 (OUTLIER) cc_final: 0.3040 (ttp)
REVERT: B  243 MET cc_start: 0.7100 (tpp) cc_final: 0.6709 (tpp)
REVERT: B  260 THR cc_start: 0.8020 (m) cc_final: 0.7693 (m)
REVERT: B  305 CYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7534 (p)
REVERT: B  307 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7173 (t80)
REVERT: C   51 LEU cc_start: 0.7991 (pp) cc_final: 0.7743 (pp)
REVERT: C  171 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8047 (mt)
REVERT: C  175 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7869 (mm-40)
REVERT: C  237 ASN cc_start: 0.7592 (t0) cc_final: 0.7364 (t0)
REVERT: C  280 LYS cc_start: 0.6734 (tttt) cc_final: 0.6449 (mtpp)
REVERT: P    3 ASN cc_start: 0.6388 (p0) cc_final: 0.6132 (p0)
REVERT: P    7 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7966 (ptp90)
REVERT: S  140 MET cc_start: 0.4155 (ptp) cc_final: 0.2585 (tpt)
  outliers start: 53
  outliers final: 22
  residues processed: 223
  average time/residue: 0.0963
  time to fit residues: 29.1361
Evaluate side-chains
  205 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 176
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   59 VAL
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  240 MET
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   86 THR
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  142 HIS
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain P residue    7 ARG
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue  172 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.201149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.161380 restraints weight = 14361.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.4021 rms_B_bonded: 3.21
r_work: 0.3843 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9222  Z= 0.156
  Angle     :  0.642   8.281  12495  Z= 0.326
  Chirality :  0.043   0.186   1414
  Planarity :  0.004   0.049   1577
  Dihedral  :  4.726  40.139   1250
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 27.74 %
    Favored  : 67.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.25), residues: 1128
  helix:  1.85 (0.27), residues: 376
  sheet:  0.44 (0.31), residues: 275
  loop : -1.49 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 184 
 TYR   0.012   0.001   TYR S 235 
 PHE   0.013   0.001   PHE A 221 
 TRP   0.013   0.002   TRP C  63 
 HIS   0.013   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9221)
  covalent geometry    : angle       0.63975 (12493)
  SS BOND              : bond        0.01093 (    1)
  SS BOND              : angle       4.13976 (    2)
  hydrogen bonds       : bond        0.05460 (  420)
  hydrogen bonds       : angle       4.31293 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 181
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.6058 (ppp) cc_final: 0.5709 (ppp)
REVERT: A  170 LEU cc_start: 0.7590 (tm) cc_final: 0.7056 (tp)
REVERT: A  180 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7122 (tp)
REVERT: A  205 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6211 (mt-10)
REVERT: A  281 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6959 (mp)
REVERT: A  332 PHE cc_start: 0.7389 (m-10) cc_final: 0.7095 (m-10)
REVERT: B   20 ASP cc_start: 0.7280 (m-30) cc_final: 0.6800 (m-30)
REVERT: B  209 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7700 (ttpt)
REVERT: B  260 THR cc_start: 0.8092 (m) cc_final: 0.7779 (m)
REVERT: B  307 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7166 (t80)
REVERT: C   51 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7673 (pp)
REVERT: C  161 SER cc_start: 0.8477 (t) cc_final: 0.8225 (t)
REVERT: C  175 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7861 (mm-40)
REVERT: C  237 ASN cc_start: 0.7695 (t0) cc_final: 0.7438 (t0)
REVERT: C  304 ARG cc_start: 0.7097 (ttp80) cc_final: 0.6792 (ttm170)
REVERT: C  340 ASN cc_start: 0.7736 (t0) cc_final: 0.7521 (t0)
REVERT: S   93 MET cc_start: 0.4106 (pmm) cc_final: 0.3662 (ptt)
REVERT: S  140 MET cc_start: 0.4145 (ptp) cc_final: 0.2552 (tpt)
  outliers start: 44
  outliers final: 26
  residues processed: 209
  average time/residue: 0.0898
  time to fit residues: 25.2570
Evaluate side-chains
  207 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 176
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   50 THR
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  252 LEU
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue  172 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 8 optimal weight:    0.4980
   chunk 60 optimal weight:    0.0270
   chunk 58 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0980
   chunk 67 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.3638

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 HIS
C 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.202684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.164005 restraints weight = 14550.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.15
r_work: 0.3885 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9222  Z= 0.114
  Angle     :  0.590   9.654  12495  Z= 0.297
  Chirality :  0.042   0.210   1414
  Planarity :  0.003   0.043   1577
  Dihedral  :  4.321  32.212   1250
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 27.03 %
    Favored  : 68.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.25), residues: 1128
  helix:  2.11 (0.27), residues: 375
  sheet:  0.65 (0.32), residues: 270
  loop : -1.49 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 314 
 TYR   0.015   0.001   TYR S 235 
 PHE   0.011   0.001   PHE C 199 
 TRP   0.013   0.001   TRP C 297 
 HIS   0.003   0.001   HIS C 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9221)
  covalent geometry    : angle       0.58813 (12493)
  SS BOND              : bond        0.00503 (    1)
  SS BOND              : angle       3.59821 (    2)
  hydrogen bonds       : bond        0.04402 (  420)
  hydrogen bonds       : angle       3.99957 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 183
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 VAL cc_start: 0.7071 (t) cc_final: 0.6822 (t)
REVERT: A   80 MET cc_start: 0.5981 (ppp) cc_final: 0.5681 (ppp)
REVERT: A  170 LEU cc_start: 0.7475 (tm) cc_final: 0.6981 (tp)
REVERT: A  205 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5905 (mt-10)
REVERT: A  332 PHE cc_start: 0.7338 (m-10) cc_final: 0.7012 (m-10)
REVERT: B   17 LYS cc_start: 0.7264 (mmtp) cc_final: 0.7043 (mmmm)
REVERT: B   25 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7537 (tm-30)
REVERT: B  209 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7657 (ttpt)
REVERT: B  243 MET cc_start: 0.7349 (tpp) cc_final: 0.7066 (tpp)
REVERT: B  260 THR cc_start: 0.8111 (m) cc_final: 0.7830 (m)
REVERT: B  305 CYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7567 (p)
REVERT: B  307 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7173 (t80)
REVERT: C  168 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7844 (tp)
REVERT: C  169 TRP cc_start: 0.8188 (OUTLIER) cc_final: 0.6686 (p90)
REVERT: C  171 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8006 (mm)
REVERT: C  175 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7799 (mm-40)
REVERT: C  237 ASN cc_start: 0.7656 (t0) cc_final: 0.7439 (t0)
REVERT: C  259 GLN cc_start: 0.7619 (pm20) cc_final: 0.7371 (pt0)
REVERT: C  267 ASP cc_start: 0.7306 (m-30) cc_final: 0.7065 (m-30)
REVERT: C  340 ASN cc_start: 0.7619 (t0) cc_final: 0.7312 (t0)
REVERT: S   79 LEU cc_start: 0.3538 (OUTLIER) cc_final: 0.3251 (tt)
REVERT: S   93 MET cc_start: 0.4123 (pmm) cc_final: 0.3867 (ptt)
REVERT: S  140 MET cc_start: 0.3977 (ptp) cc_final: 0.2318 (tpt)
  outliers start: 47
  outliers final: 30
  residues processed: 214
  average time/residue: 0.1021
  time to fit residues: 29.4190
Evaluate side-chains
  214 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain S residue   52 SER
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue  172 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    0.0970
   chunk 90 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 HIS
C 110 ASN
C 340 ASN
D  42 GLN
D  90 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.199047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.161108 restraints weight = 14373.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 3.21
r_work: 0.3826 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   9222  Z= 0.141
  Angle     :  0.644  10.818  12495  Z= 0.322
  Chirality :  0.043   0.204   1414
  Planarity :  0.004   0.046   1577
  Dihedral  :  4.470  38.888   1247
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 26.83 %
    Favored  : 67.28 %
  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 are not related in a simple way.
  whole:  0.35 (0.25), residues: 1128
  helix:  2.03 (0.27), residues: 375
  sheet:  0.66 (0.32), residues: 270
  loop : -1.56 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 314 
 TYR   0.015   0.001   TYR S 235 
 PHE   0.011   0.001   PHE C 199 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.004   0.001   HIS C 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9221)
  covalent geometry    : angle       0.64194 (12493)
  SS BOND              : bond        0.00592 (    1)
  SS BOND              : angle       3.65242 (    2)
  hydrogen bonds       : bond        0.05194 (  420)
  hydrogen bonds       : angle       4.19218 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 179
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 VAL cc_start: 0.7144 (t) cc_final: 0.6877 (t)
REVERT: A   74 MET cc_start: 0.6481 (mmt) cc_final: 0.6174 (mmt)
REVERT: A   80 MET cc_start: 0.6133 (ppp) cc_final: 0.5798 (ppp)
REVERT: A  170 LEU cc_start: 0.7435 (tm) cc_final: 0.6963 (tp)
REVERT: A  205 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6030 (mt-10)
REVERT: A  281 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7033 (mp)
REVERT: A  332 PHE cc_start: 0.7561 (m-10) cc_final: 0.7259 (m-10)
REVERT: B   17 LYS cc_start: 0.7451 (mmtp) cc_final: 0.7192 (mmmm)
REVERT: B   20 ASP cc_start: 0.7414 (m-30) cc_final: 0.7011 (m-30)
REVERT: B   21 ARG cc_start: 0.7895 (tmm-80) cc_final: 0.7635 (ttp80)
REVERT: B  209 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7703 (ttpt)
REVERT: B  243 MET cc_start: 0.7379 (tpp) cc_final: 0.7063 (tpp)
REVERT: B  260 THR cc_start: 0.8127 (m) cc_final: 0.7846 (m)
REVERT: C   10 GLU cc_start: 0.8138 (tp30) cc_final: 0.7723 (tp30)
REVERT: C   14 LEU cc_start: 0.7584 (tt) cc_final: 0.7236 (tp)
REVERT: C   48 ARG cc_start: 0.8013 (tpp80) cc_final: 0.7782 (tpp80)
REVERT: C   83 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7366 (t0)
REVERT: C  168 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7892 (tp)
REVERT: C  171 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8057 (mm)
REVERT: C  175 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7907 (mm-40)
REVERT: C  237 ASN cc_start: 0.7586 (t0) cc_final: 0.7382 (t0)
REVERT: S   79 LEU cc_start: 0.3648 (OUTLIER) cc_final: 0.3360 (tt)
REVERT: S  140 MET cc_start: 0.4050 (ptp) cc_final: 0.2315 (tpt)
  outliers start: 58
  outliers final: 37
  residues processed: 217
  average time/residue: 0.0974
  time to fit residues: 28.4249
Evaluate side-chains
  219 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 176
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain C residue   96 ARG
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  261 LEU
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain S residue   52 SER
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  188 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 HIS
A 321 ASN
B 188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.196235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.155999 restraints weight = 14296.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3964 rms_B_bonded: 3.06
r_work: 0.3808 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9222  Z= 0.167
  Angle     :  0.658   9.534  12495  Z= 0.334
  Chirality :  0.044   0.202   1414
  Planarity :  0.004   0.058   1577
  Dihedral  :  4.651  42.645   1247
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 26.73 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.25), residues: 1128
  helix:  1.99 (0.27), residues: 375
  sheet:  0.67 (0.32), residues: 263
  loop : -1.69 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 184 
 TYR   0.015   0.001   TYR S 235 
 PHE   0.013   0.001   PHE C 151 
 TRP   0.013   0.002   TRP C 297 
 HIS   0.010   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 9221)
  covalent geometry    : angle       0.65681 (12493)
  SS BOND              : bond        0.00673 (    1)
  SS BOND              : angle       3.73342 (    2)
  hydrogen bonds       : bond        0.05487 (  420)
  hydrogen bonds       : angle       4.28655 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 182
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 VAL cc_start: 0.7078 (t) cc_final: 0.6829 (p)
REVERT: A   74 MET cc_start: 0.6424 (mmt) cc_final: 0.6123 (mmt)
REVERT: A   80 MET cc_start: 0.6060 (ppp) cc_final: 0.5743 (ppp)
REVERT: A  170 LEU cc_start: 0.7460 (tm) cc_final: 0.7238 (tt)
REVERT: A  190 MET cc_start: 0.4186 (OUTLIER) cc_final: 0.3866 (ptm)
REVERT: A  205 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6190 (mt-10)
REVERT: A  219 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8257 (t)
REVERT: A  271 MET cc_start: 0.6214 (tpp) cc_final: 0.5982 (tpp)
REVERT: A  278 PHE cc_start: 0.6937 (t80) cc_final: 0.6648 (t80)
REVERT: A  332 PHE cc_start: 0.7671 (m-10) cc_final: 0.7438 (m-80)
REVERT: B   17 LYS cc_start: 0.7520 (mmtp) cc_final: 0.7290 (mmmm)
REVERT: B  209 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7726 (ttpt)
REVERT: B  243 MET cc_start: 0.7452 (tpp) cc_final: 0.7163 (tpp)
REVERT: B  260 THR cc_start: 0.8125 (m) cc_final: 0.7838 (m)
REVERT: C   10 GLU cc_start: 0.8174 (tp30) cc_final: 0.7922 (tp30)
REVERT: C  171 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8102 (mt)
REVERT: C  175 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7913 (mm-40)
REVERT: C  237 ASN cc_start: 0.7622 (t0) cc_final: 0.7417 (t0)
REVERT: S   79 LEU cc_start: 0.3883 (OUTLIER) cc_final: 0.3634 (tt)
REVERT: S  140 MET cc_start: 0.3988 (ptp) cc_final: 0.2320 (tpt)
  outliers start: 58
  outliers final: 40
  residues processed: 221
  average time/residue: 0.0820
  time to fit residues: 24.5749
Evaluate side-chains
  226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 181
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  205 GLU
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   96 ARG
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain D residue   46 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain S residue   79 LEU
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  188 LEU
Chi-restraints excluded: chain S residue  195 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 61 optimal weight:    0.0370
   chunk 108 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0980
   chunk 58 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
** A  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 HIS
B 188 HIS
C 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.196936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.158809 restraints weight = 14437.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 3.17
r_work: 0.3835 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9222  Z= 0.127
  Angle     :  0.615   8.798  12495  Z= 0.312
  Chirality :  0.042   0.198   1414
  Planarity :  0.004   0.046   1577
  Dihedral  :  4.471  37.399   1247
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 27.34 %
    Favored  : 67.68 %
  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 are not related in a simple way.
  whole:  0.28 (0.25), residues: 1128
  helix:  2.06 (0.27), residues: 374
  sheet:  0.58 (0.32), residues: 268
  loop : -1.63 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 184 
 TYR   0.009   0.001   TYR S 190 
 PHE   0.014   0.001   PHE A 221 
 TRP   0.015   0.001   TRP C 297 
 HIS   0.011   0.001   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9221)
  covalent geometry    : angle       0.61317 (12493)
  SS BOND              : bond        0.00576 (    1)
  SS BOND              : angle       3.49259 (    2)
  hydrogen bonds       : bond        0.04731 (  420)
  hydrogen bonds       : angle       4.16055 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 191
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 VAL cc_start: 0.6951 (t) cc_final: 0.6685 (t)
REVERT: A   74 MET cc_start: 0.6401 (mmt) cc_final: 0.6111 (mmt)
REVERT: A   80 MET cc_start: 0.6015 (ppp) cc_final: 0.5672 (ppp)
REVERT: A  170 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6929 (tp)
REVERT: A  190 MET cc_start: 0.4268 (OUTLIER) cc_final: 0.3939 (ptm)
REVERT: A  219 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8272 (t)
REVERT: A  281 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7131 (mp)
REVERT: A  332 PHE cc_start: 0.7602 (m-10) cc_final: 0.7377 (m-80)
REVERT: B   17 LYS cc_start: 0.7471 (mmtp) cc_final: 0.7145 (mmmm)
REVERT: B   20 ASP cc_start: 0.7332 (m-30) cc_final: 0.7017 (m-30)
REVERT: B   21 ARG cc_start: 0.7796 (tmm-80) cc_final: 0.7562 (ttp80)
REVERT: B  209 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7709 (ttpt)
REVERT: B  243 MET cc_start: 0.7419 (tpp) cc_final: 0.7087 (tpp)
REVERT: B  260 THR cc_start: 0.8103 (m) cc_final: 0.7828 (m)
REVERT: B  307 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7375 (t80)
REVERT: C   10 GLU cc_start: 0.8116 (tp30) cc_final: 0.7871 (tp30)
REVERT: C  128 THR cc_start: 0.8339 (t) cc_final: 0.8004 (p)
REVERT: C  168 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7846 (tp)
REVERT: C  171 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8037 (mm)
REVERT: C  175 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7801 (mm-40)
REVERT: C  234 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8106 (t80)
REVERT: C  237 ASN cc_start: 0.7612 (t0) cc_final: 0.7393 (t0)
REVERT: C  314 ARG cc_start: 0.7641 (ttm170) cc_final: 0.7439 (ttm170)
REVERT: C  327 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7498 (t)
REVERT: D   69 MET cc_start: 0.3254 (ptp) cc_final: 0.2927 (ptp)
REVERT: S   34 MET cc_start: 0.3513 (mtp) cc_final: 0.3265 (mmm)
REVERT: S  140 MET cc_start: 0.3959 (ptp) cc_final: 0.2312 (tpt)
  outliers start: 49
  outliers final: 34
  residues processed: 225
  average time/residue: 0.0860
  time to fit residues: 25.9031
Evaluate side-chains
  225 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 182
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  116 CYS
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   96 ARG
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain S residue  188 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  37 GLN
** A  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 304 HIS
B  52 GLN
B 188 HIS
S 232 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.192163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.152874 restraints weight = 14102.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 3.04
r_work: 0.3763 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9222  Z= 0.185
  Angle     :  0.705  10.803  12495  Z= 0.358
  Chirality :  0.045   0.193   1414
  Planarity :  0.004   0.043   1577
  Dihedral  :  4.910  47.296   1247
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 27.54 %
    Favored  : 67.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.25), residues: 1128
  helix:  1.95 (0.27), residues: 374
  sheet:  0.61 (0.31), residues: 267
  loop : -1.68 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 314 
 TYR   0.010   0.001   TYR S 102 
 PHE   0.017   0.002   PHE A 221 
 TRP   0.013   0.002   TRP C 297 
 HIS   0.010   0.002   HIS A 304 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 9221)
  covalent geometry    : angle       0.70371 (12493)
  SS BOND              : bond        0.00799 (    1)
  SS BOND              : angle       3.93480 (    2)
  hydrogen bonds       : bond        0.05957 (  420)
  hydrogen bonds       : angle       4.52420 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 187
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7979 (m-80)
REVERT: A   64 VAL cc_start: 0.7035 (t) cc_final: 0.6806 (p)
REVERT: A   74 MET cc_start: 0.6413 (mmt) cc_final: 0.6182 (mmt)
REVERT: A   80 MET cc_start: 0.6051 (ppp) cc_final: 0.5729 (ppp)
REVERT: A  190 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4665 (ptm)
REVERT: A  219 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8313 (t)
REVERT: A  278 PHE cc_start: 0.7058 (t80) cc_final: 0.6734 (t80)
REVERT: B  260 THR cc_start: 0.8132 (m) cc_final: 0.7833 (m)
REVERT: C   10 GLU cc_start: 0.8143 (tp30) cc_final: 0.7832 (tp30)
REVERT: C  128 THR cc_start: 0.8352 (t) cc_final: 0.8113 (p)
REVERT: C  168 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7941 (tp)
REVERT: C  171 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8136 (mt)
REVERT: C  237 ASN cc_start: 0.7643 (t0) cc_final: 0.7438 (t0)
REVERT: C  325 MET cc_start: 0.6661 (ppp) cc_final: 0.6252 (ppp)
REVERT: S   93 MET cc_start: 0.3665 (pmm) cc_final: 0.2227 (ptt)
REVERT: S  140 MET cc_start: 0.4061 (ptp) cc_final: 0.2006 (tmm)
  outliers start: 52
  outliers final: 38
  residues processed: 220
  average time/residue: 0.0956
  time to fit residues: 28.1377
Evaluate side-chains
  229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 186
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   46 PHE
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   96 ARG
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  301 LYS
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  188 LEU
Chi-restraints excluded: chain S residue  195 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
B  52 GLN
B 188 HIS
D  42 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.193970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.153925 restraints weight = 14213.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 2.66
r_work: 0.3811 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9222  Z= 0.144
  Angle     :  0.670   9.840  12495  Z= 0.336
  Chirality :  0.043   0.195   1414
  Planarity :  0.004   0.041   1577
  Dihedral  :  4.697  41.523   1247
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 28.35 %
    Favored  : 67.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.21 (0.25), residues: 1128
  helix:  1.98 (0.27), residues: 375
  sheet:  0.51 (0.31), residues: 277
  loop : -1.67 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 314 
 TYR   0.009   0.001   TYR S 102 
 PHE   0.015   0.001   PHE A 221 
 TRP   0.015   0.001   TRP C 297 
 HIS   0.003   0.001   HIS C 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 9221)
  covalent geometry    : angle       0.66836 (12493)
  SS BOND              : bond        0.00802 (    1)
  SS BOND              : angle       3.19776 (    2)
  hydrogen bonds       : bond        0.04979 (  420)
  hydrogen bonds       : angle       4.33292 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 182
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8020 (tt) cc_final: 0.7704 (tp)
REVERT: A   64 VAL cc_start: 0.6995 (t) cc_final: 0.6746 (t)
REVERT: A   80 MET cc_start: 0.5874 (ppp) cc_final: 0.5579 (ppp)
REVERT: A  170 LEU cc_start: 0.7303 (tt) cc_final: 0.7100 (tp)
REVERT: A  190 MET cc_start: 0.4883 (OUTLIER) cc_final: 0.4628 (ptm)
REVERT: A  219 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8216 (t)
REVERT: A  281 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7197 (mp)
REVERT: B   21 ARG cc_start: 0.7759 (tmm-80) cc_final: 0.7551 (ttp80)
REVERT: B   25 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7491 (tm-30)
REVERT: B   32 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7223 (mtm110)
REVERT: B  209 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7719 (ttpt)
REVERT: B  251 ASP cc_start: 0.7979 (t0) cc_final: 0.7773 (t0)
REVERT: B  260 THR cc_start: 0.8113 (m) cc_final: 0.7816 (m)
REVERT: C   10 GLU cc_start: 0.8091 (tp30) cc_final: 0.7679 (tp30)
REVERT: C  168 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7900 (tp)
REVERT: C  171 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (mt)
REVERT: C  175 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7882 (mm-40)
REVERT: C  314 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7399 (ttm170)
REVERT: S  140 MET cc_start: 0.4005 (ptp) cc_final: 0.2197 (tmm)
  outliers start: 44
  outliers final: 31
  residues processed: 215
  average time/residue: 0.0977
  time to fit residues: 28.2687
Evaluate side-chains
  218 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 181
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   96 ARG
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain S residue  188 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   chunk 64 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 108 optimal weight:    9.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
B 188 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.191670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.152065 restraints weight = 14076.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.67
r_work: 0.3788 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.5035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9222  Z= 0.161
  Angle     :  0.710  11.036  12495  Z= 0.354
  Chirality :  0.045   0.220   1414
  Planarity :  0.004   0.040   1577
  Dihedral  :  4.847  43.371   1247
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 28.56 %
    Favored  : 67.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.25), residues: 1128
  helix:  1.95 (0.26), residues: 374
  sheet:  0.48 (0.30), residues: 274
  loop : -1.76 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 314 
 TYR   0.016   0.001   TYR S 235 
 PHE   0.017   0.001   PHE A  46 
 TRP   0.015   0.002   TRP C 297 
 HIS   0.009   0.001   HIS S 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 9221)
  covalent geometry    : angle       0.70910 (12493)
  SS BOND              : bond        0.00759 (    1)
  SS BOND              : angle       3.41343 (    2)
  hydrogen bonds       : bond        0.05415 (  420)
  hydrogen bonds       : angle       4.37603 ( 1203)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8042 (tt) cc_final: 0.7773 (tp)
REVERT: A   64 VAL cc_start: 0.7066 (t) cc_final: 0.6852 (p)
REVERT: A   80 MET cc_start: 0.5834 (ppp) cc_final: 0.5525 (ppp)
REVERT: A  190 MET cc_start: 0.4976 (OUTLIER) cc_final: 0.4649 (ptm)
REVERT: A  219 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8236 (t)
REVERT: B   21 ARG cc_start: 0.7744 (tmm-80) cc_final: 0.7539 (ttp80)
REVERT: B   25 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7502 (tm-30)
REVERT: B   32 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7283 (mtm110)
REVERT: B   52 GLN cc_start: 0.8195 (mt0) cc_final: 0.7954 (mt0)
REVERT: B  260 THR cc_start: 0.8123 (m) cc_final: 0.7817 (m)
REVERT: C   45 MET cc_start: 0.8067 (mtm) cc_final: 0.7835 (mtm)
REVERT: C  168 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7925 (tp)
REVERT: C  171 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8101 (mt)
REVERT: C  314 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7441 (ttm170)
REVERT: S   57 THR cc_start: 0.7636 (p) cc_final: 0.7425 (p)
REVERT: S   93 MET cc_start: 0.3626 (pmm) cc_final: 0.2346 (ptt)
REVERT: S  140 MET cc_start: 0.3810 (ptp) cc_final: 0.1882 (tmm)
  outliers start: 42
  outliers final: 35
  residues processed: 217
  average time/residue: 0.0960
  time to fit residues: 27.6182
Evaluate side-chains
  227 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 187
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 SER
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  203 CYS
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  222 SER
Chi-restraints excluded: chain A residue  223 HIS
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  327 ILE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue   32 ARG
Chi-restraints excluded: chain B residue  184 ILE
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  353 LEU
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   18 ILE
Chi-restraints excluded: chain C residue   96 ARG
Chi-restraints excluded: chain C residue   98 SER
Chi-restraints excluded: chain C residue  168 LEU
Chi-restraints excluded: chain C residue  169 TRP
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain C residue  195 ASP
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  278 PHE
Chi-restraints excluded: chain C residue  296 VAL
Chi-restraints excluded: chain C residue  327 VAL
Chi-restraints excluded: chain P residue    4 LEU
Chi-restraints excluded: chain S residue  246 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0470
   chunk 80 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0070
   chunk 82 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0070
   chunk 23 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0870
   overall best weight:    0.1892

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.196020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.157702 restraints weight = 14036.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 2.64
r_work: 0.3850 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9222  Z= 0.116
  Angle     :  0.649   9.859  12495  Z= 0.321
  Chirality :  0.043   0.187   1414
  Planarity :  0.003   0.038   1577
  Dihedral  :  4.431  32.425   1247
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 30.18 %
    Favored  : 66.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.25), residues: 1128
  helix:  2.13 (0.27), residues: 373
  sheet:  0.37 (0.31), residues: 280
  loop : -1.59 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  48 
 TYR   0.014   0.001   TYR B 230 
 PHE   0.012   0.001   PHE A 221 
 TRP   0.017   0.001   TRP C 297 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 9221)
  covalent geometry    : angle       0.64802 (12493)
  SS BOND              : bond        0.00421 (    1)
  SS BOND              : angle       2.88087 (    2)
  hydrogen bonds       : bond        0.04018 (  420)
  hydrogen bonds       : angle       4.06752 ( 1203)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2406.09 seconds
wall clock time: 41 minutes 50.05 seconds (2510.05 seconds total)